Differential knockout of a heterozygous allele of samd9

ABSTRACT

RNA molecules comprising a guide sequence portion having 17-50 contiguous nucleotides containing nucleotides in the sequence set forth in any one of SEQ ID NOs: 1-20640 and compositions, methods, and uses thereof.

Throughout this application, various publications are referenced,including referenced in parenthesis. The disclosures of all publicationsmentioned in this application in their entireties are herebyincorporated by reference into this application in order to provideadditional description of the art to which this invention pertains andof the features in the art which can be employed with this invention.

REFERENCE TO SEQUENCE LISTING

This application incorporates-by-reference nucleotide sequences whichare present in the file named“210528_91330-A-PCT_Sequence_Listing_AWG.txt”, which is 4,392 kilobytesin size, and which was created on May 27, 2021 in the IBM-PC machineformat, having an operating system compatibility with MS-Windows, whichis contained in the text file filed May 28, 2021 as part of thisapplication.

BACKGROUND OF INVENTION

There are several classes of DNA variation in the human genome,including insertions and deletions, differences in the copy number ofrepeated sequences, and single nucleotide polymorphisms (SNPs). A SNP isa DNA sequence variation occurring when a single nucleotide (adenine(A), thymine (T), cytosine (C), or guanine (G)) in the genome differsbetween human subjects or paired chromosomes in an individual. Over theyears, the different types of DNA variations have been the focus of theresearch community either as markers in studies to pinpoint traits ordisease causation or as potential causes of genetic disorders.

A genetic disorder is caused by one or more abnormalities in the genome.Genetic disorders may be regarded as either “dominant” or “recessive.”Recessive genetic disorders are those which require two copies (i.e.,two alleles) of the abnormal/defective gene to be present. In contrast,a dominant genetic disorder involves a gene or genes which exhibit(s)dominance over a normal (functional/healthy) gene or genes. As such, indominant genetic disorders only a single copy (i.e., allele) of anabnormal gene is required to cause or contribute to the symptoms of aparticular genetic disorder. Such mutations include, for example,gain-of-function mutations in which the altered gene product possesses anew molecular function or a new pattern of gene expression. Otherexamples include dominant negative mutations, which have a gene productthat acts antagonistically to the wild-type allele.

MIRAGE SYNDROME

Sterile alpha motif domain containing 9 (SAMD9) is a protein encodinggene that is involved in control of cell proliferation and functions asa tumor suppressor in some cancers (Davidsson et al., 2018). Severaldominant negative mutations of the SAMD9 gene were shown to beassociated with MIRAGE syndrome, which is a rare disorder that manifestsas a form of syndromic adrenal hypoplasia, characterized bymyelodysplasia, infection, restriction of growth, adrenal hypoplasia,genital phenotypes, and enteropathy (Narumi et al., 2016).

SUMMARY OF THE INVENTION

Disclosed is an approach for knocking out the expression of adominant-mutated allele by disrupting the dominant-mutated allele ordegrading the resulting mRNA.

The present disclosure provides a method for utilizing at least onenaturally occurring nucleotide difference or polymorphism (e.g., singlenucleotide polymorphism (SNP)) for distinguishing/discriminating betweentwo alleles of a gene, one allele bearing a mutation such that itencodes a mutated protein causing a disease phenotype (“mutated allele”)and a particular sequence in a SNP position (REF/SNP), and the otherallele encoding for a functional protein (“functional allele”). In someembodiments, the SNP position is utilized fordistinguishing/discriminating between two alleles of a gene bearing oneor more disease associated mutations, such as to target one of thealleles bearing both the particular sequence in the SNP position(SNP/REF) and a disease associated mutation. In some embodiments, thedisease-associated mutation is targeted. In some embodiments, the methodfurther comprises the step of knocking out expression of the mutatedprotein and allowing expression of the functional protein.

The present disclosure also provides a method for modifying in a cell amutant allele of the sterile alpha motif domain containing 9 (SAMD9)gene having a mutation associated with MIRAGE syndrome, the methodcomprising introducing to the cell a composition comprising:

-   a CRISPR nuclease or a sequence encoding the CRISPR nuclease; and-   a first RNA molecule comprising a guide sequence portion having    17-50 nucleotides or a nucleotide sequence encoding the same,

wherein a complex of the CRISPR nuclease and the first RNA moleculeaffects a double strand break in the mutant allele of the SAMD9 gene.

According to embodiments of the present invention, there is provided afirst RNA molecule comprising a guide sequence portion having 17-50contiguous nucleotides containing nucleotides in the sequence set forthin any one of SEQ ID Nos: 1-20640.

According to some embodiments of the present invention, there isprovided a composition comprising an RNA molecule comprising a guidesequence portion having 17-50 contiguous nucleotides containingnucleotides in the sequence set forth in any one of SEQ ID NOs: 1-20640and a CRISPR nuclease.

According to some embodiments of the present invention, there isprovided a method for inactivating a mutant SAMD9 allele in a cell, themethod comprising delivering to the cell a composition comprising an RNAmolecule comprising a guide sequence portion having 17-50 contiguousnucleotides containing nucleotides in the sequence set forth in any oneof SEQ ID NOs: 1-20640 and a CRISPR nuclease. In some embodiments, thecell is a stem cell. In some embodiments, the stem cell is ahematopoietic stem/progenitor cell (HSC). In some embodiments, thedelivering to the cell is performed in vitro, ex vivo, or in vivo. Insome embodiments, the method is performed ex vivo and the cell isprovided/explanted from an individual patient. In some embodiments, themethod further comprises the step of introducing the resulting cell,with the modified/knocked out mutant SAMD9 allele, into the individualpatient (e.g. autologous transplantation).

According to some embodiments of the present invention, there isprovided a method for treating MIRAGE syndrome, the method comprisingdelivering to a cell of a subject having MIRAGE syndrome a compositioncomprising an RNA molecule comprising a guide sequence portion having17-50 contiguous nucleotides containing nucleotides in the sequence setforth in any one of SEQ ID NOs: 1-20640 and a CRISPR nuclease.

According to some embodiments of the present invention, there isprovided use of a composition comprising an RNA molecule comprising aguide sequence portion having 17-50 contiguous nucleotides containingnucleotides in the sequence set forth in any one of SEQ ID NOs: 1-20640and a CRISPR nuclease for inactivating a mutant SAMD9 allele in a cell,comprising delivering to the cell the composition comprising an RNAmolecule comprising a guide sequence portion having 17-50 contiguousnucleotides containing nucleotides in the sequence set forth in any oneof SEQ ID NOs: 1-20640 and a CRISPR nuclease.

According to embodiments of the present invention, there is provided amedicament comprising an RNA molecule comprising a guide sequenceportion having 17-50 contiguous nucleotides containing nucleotides inthe sequence set forth in any one of SEQ ID NOs: 1-20640 and a CRISPRnuclease for use in inactivating a mutant SAMD9 allele in a cell,wherein the medicament is administered by delivering to the cell thecomposition comprising an RNA molecule comprising a guide sequenceportion having 17-50 contiguous nucleotides containing nucleotides inthe sequence set forth in any one of SEQ ID NOs: 1-20640 and a CRISPRnuclease.

According to some embodiments of the present invention, there isprovided use of a composition comprising an RNA molecule comprising aguide sequence portion having 17-50 contiguous nucleotides containingnucleotides in the sequence set forth in any one of SEQ ID NOs: 1-20640and a CRISPR nuclease for treating ameliorating or preventing MIRAGEsyndrome, comprising delivering to a cell of a subject having or at riskof having MIRAGE syndrome the composition of comprising an RNA moleculecomprising a guide sequence portion having 17-50 contiguous nucleotidescontaining nucleotides in the sequence set forth in any one of SEQ IDNOs: 1-20640 and a CRISPR nuclease. In some embodiments, the method isperformed ex vivo and the cell is provided/explanted from the subject.In some embodiments, the method further comprises the step ofintroducing the resulting cell, with the modified/knocked out mutantSAMD9 allele, into the subject (e.g. autologous transplantation).

According to some embodiments of the present invention, there isprovided a medicament comprising the composition comprising an RNAmolecule comprising a guide sequence portion having 17-50 contiguousnucleotides containing nucleotides in the sequence set forth in any oneof SEQ ID NOs: 1-20640 and a CRISPR nuclease for use in treatingameliorating or preventing MIRAGE syndrome, wherein the medicament isadministered by delivering to a cell of a subject having or at risk ofhaving MIRAGE syndrome the composition comprising an RNA moleculecomprising a guide sequence portion having 17-50 contiguous nucleotidescontaining nucleotides in the sequence set forth in any one of SEQ IDNOs: 1-20640 and a CRISPR nuclease.

According to some embodiments of the present invention, there isprovided a kit for inactivating a mutant SAMD9 allele in a cell,comprising an RNA molecule comprising a guide sequence portion having17-50 contiguous nucleotides containing nucleotides in the sequence setforth in any one of SEQ ID NOs: 1-20640, a CRISPR nuclease, and/or atracrRNA molecule; and instructions for delivering the RNA molecule;CRISPR nuclease, and/or the tracrRNA to the cell.

According to some embodiments of the present invention, there isprovided a kit for treating MIRAGE syndrome in a subject, comprising anRNA molecule comprising a guide sequence portion having 17-50 contiguousnucleotides containing nucleotides in the sequence set forth in any oneof SEQ ID NOs: 1-20640, a CRISPR nuclease, and/or a tracrRNA molecule;and instructions for delivering the RNA molecule; CRISPR nuclease,and/or the tracrRNA to a cell of a subject having or at risk of havingMIRAGE syndrome.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 : Guide activity of RNA guide molecules targeting SAMD9 in HeLacells. An RNA guide molecule was co-transfected with SpCas9 to determinetheir on-target activity. Cells were harvested 72 hours post DNAtransfection, genomic was DNA extracted, and the region of the mutationwas amplified and analyzed by next-generation sequencing (NGS). Thegraph represents the % editing ± standard deviation (STDV) of three (3)independent transfections.

FIG. 2 : Guide activity of novel OMNI CRISPR nucleases with RNA guidemolecules targeting SAMD9 in HeLa cells. An RNA guide moleculewas-co-transfected with each OMNI CRISPR nuclease to determine itson-target activity. Cells were harvested 72 hours post DNA transfection,genomic DNA was extracted, and the region of the mutation was amplifiedand analyzed by NGS. Transfection efficiency is measured by mCherryfluorescence. The graph represents the % editing ± STDV of three (3)independent transfections.

FIG. 3 : Guide activity of RNA guide molecules targeting SAMD9 indonor-derived HSCs. RNPs complexed with SpCas9 and an RNA guide moleculewere electroporated into HSCs to determine their activity. Cells wereharvested 72 hours post RNP electroporation, genomic was DNA extracted,and the region of the mutation was amplified and analyzed by NGS. Thegraph represents the % editing ± STDV of two (2) independentelectroporations. The table below the graph indicates the genotype ofthe HSCs for each SNP.

FIGS. 4A-4B: Effect of editing on protein levels of SAMD9 in U2OS cells.RNPs complexed with SpCas9 and a RNA guide molecule were electroporatedinto U2OSs. Cells were harvested six days post RNP electroporation,cells were lysed and analyzed by western blot (WB) assay (FIG. 4A).Relative protein levels to control (NT1 - control) were quantified foreach sample (FIG. 4B).

FIGS. 5A-5D: Knockout strategies utilizing guides targeting SAMD9 -Schematic representation of example SAMD9 editing strategies. The SAMD9protein-encoding exon is represented as a white box, the UTR regions arerepresented as dotted boxes, introns are represented as black lines, anuclease is represented by scissors accompanied by an arrow thatindicates the target site, a SNP is represented by a black star, apolyadenylation signal is represented by a black triangle, and atemplate encoding a splice acceptor is represented by a striped box.FIG. 5A: Strategy 1 - Creation of a frameshift generated by the use of asingle discriminatory guide RNA molecule targeting a SNP within amutated allele of a SAMD9 coding exon. FIG. 5B: Strategy 2 - Excision ofthe mutated SAMD9 coding exon using a first discriminatory guide RNAmolecule and a second non-discriminatory guide RNA molecule. In thedepicted schematic, the first discriminatory guide targets a SNP inIntron 2 and the second non-discriminatory guide RNA molecule targetsthe 3′UTR. In an alternative example of exon excision, the firstdiscriminatory guide targets a SNP in the 3′UTR and the secondnon-discriminatory guide RNA molecule targets Intron 2. FIG. 5C:Strategy 3 - Excision of the polyadenylation signal of a mutated SAMD9allele using a first discriminatory guide RNA molecule and a secondnon-discriminatory guide RNA molecule. FIG. 5D: Strategy 4 -Introduction of a splice acceptor site upstream of the coding exon of amutated SAMD9 allele upon targeting a CRISPR nuclease to Intron 2 of themutated allele using a discriminatory guide RNA molecule.

DETAILED DESCRIPTION

Unless otherwise defined, all technical and/or scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which the invention pertains. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of embodiments of the invention, exemplarymethods and/or materials are described below. In case of conflict, thepatent specification, including definitions, will control. In addition,the materials, methods, and examples are illustrative only and are notintended to be necessarily limiting.

It should be understood that the terms “a” and “an” as used above andelsewhere herein refer to “one or more” of the enumerated components. Itwill be clear to one of ordinary skill in the art that the use of thesingular includes the plural unless specifically stated otherwise.Therefore, the terms “a,” “an” and “at least one” are usedinterchangeably in this application.

For purposes of better understanding the present teachings and in no waylimiting the scope of the teachings, unless otherwise indicated, allnumbers expressing quantities, percentages or proportions, and othernumerical values used in the specification and claims, are to beunderstood as being modified in all instances by the term “about.”Accordingly, unless indicated to the contrary, the numerical parametersset forth in the following specification and attached claims areapproximations that may vary depending upon the desired propertiessought to be obtained. At the very least, each numerical parametershould at least be construed in light of the number of reportedsignificant digits and by applying ordinary rounding techniques.

Unless otherwise stated, adjectives such as “substantially” and “about”modifying a condition or relationship characteristic of a feature orfeatures of an embodiment of the invention, are understood to mean thatthe condition or characteristic is defined to within tolerances that areacceptable for operation of the embodiment for an application for whichit is intended. Unless otherwise indicated, the word “or” in thespecification and claims is considered to be the inclusive “or” ratherthan the exclusive or, and indicates at least one of, or any combinationof items it conjoins.

In the description and claims of the present application, each of theverbs, “comprise,” “include” and “have” and conjugates thereof, are usedto indicate that the object or objects of the verb are not necessarily acomplete listing of components, elements or parts of the subject orsubjects of the verb. Other terms as used herein are meant to be definedby their well-known meanings in the art.

The terms “nucleic acid template” and “donor”, refer to a nucleotidesequence that is inserted or copied into a genome. The nucleic acidtemplate comprises a nucleotide sequence, e.g., of one or morenucleotides, that will be added to or will template a change in thetarget nucleic acid or may be used to modify the target sequence. Anucleic acid template sequence may be of any length, for example between2 and 10,000 nucleotides in length, preferably between about 100 and1,000 nucleotides in length, more preferably between about 200 and 500nucleotides in length. A nucleic acid template may be a single strandednucleic acid, a double stranded nucleic acid. In some embodiments, thenucleic acid template comprises a nucleotide sequence, e.g., of one ormore nucleotides, that corresponds to wild type sequence of the targetnucleic acid, e.g., of the target position. In some embodiments, thenucleic acid template comprises a nucleotide sequence, e.g., of one ormore ribonucleotides, that corresponds to wild type sequence of thetarget nucleic acid, e.g., of the target position. In some embodiments,the nucleic acid template comprises modified nucleotides.

In some embodiments of the present invention, a DNA nuclease is utilizedto affect a DNA break at a target site to induce cellular repairmechanisms, for example, but not limited to, non-homologous end-joining(NHEJ). During classical NHEJ, two ends of a double-strand break (DSB)site are ligated together in a fast but also inaccurate manner (i.e.frequently resulting in mutation of the DNA at the cleavage site in theform of small insertion or deletions) whereas during HDR, an intacthomologous DNA donor is used to replace the DNA surrounding the cleavagesite in an accurate manner. HDR can also mediate the precise insertionof exogenous DNA at the break site. Accordingly, the term“homology-directed repair” or “HDR” refers to a mechanism for repairingDNA damage in cells, for example, during repair of double-stranded andsingle-stranded breaks in DNA. HDR requires nucleotide sequence homologyand uses a “nucleic acid template” (nucleic acid template or donortemplate used interchangeably herein) to repair the sequence where thedouble-stranded or single break occurred (e.g., DNA target sequence).This results in the transfer of genetic information from, for example,the nucleic acid template to the DNA target sequence. HDR may result inalteration of the DNA target sequence (e.g., insertion, deletion,mutation) if the nucleic acid template sequence differs from the DNAtarget sequence and part or all of the nucleic acid templatepolynucleotide or oligonucleotide is incorporated into the DNA targetsequence. In some embodiments, an entire nucleic acid templatepolynucleotide, a portion of the nucleic acid template polynucleotide,or a copy of the nucleic acid template is integrated at the site of theDNA target sequence.

Insertion of an exogenous sequence (also called a “donor sequence,”donor template,” “donor molecule” or “donor”), for example, forinsertion of a splice site to knockout expression of a gene, can also becarried out. For example, donor sequence can contain a non-homologoussequence flanked by two regions of homology to allow for efficient HDRat the location of interest. Additionally, donor sequences can comprisea vector molecule containing sequences that are not homologous to theregion of interest in cellular chromatin. A donor molecule can containseveral, discontinuous regions of homology to cellular chromatin. Forexample, for targeted insertion of sequences not normally present in aregion of interest, said sequences can be present in a donor nucleicacid molecule and flanked by regions of homology to sequence in theregion of interest. A donor molecule may be any length, for exampleranging from several bases e.g. 10-20 bases to multiple kilobases inlength.

The donor polynucleotide can be DNA or RNA, single-stranded and/ordouble-stranded and can be introduced into a cell in linear or circularform. See, e.g., U.S. Pat. Publication Nos. 2010/0047805; 2011/0281361;2011/0207221; and 2019/0330620. If introduced in linear form, the endsof the donor sequence can be protected (e.g., from exonucleolyticdegradation) by methods known to those of skill in the art. For example,one or more dideoxynucleotide residues are added to the 3′ terminus of alinear molecule and/or self-complementary oligonucleotides are ligatedto one or both ends. See, for example, Chang et al. (1987) and Nehls etal. (1996). Additional methods for protecting exogenous polynucleotidesfrom degradation include, but are not limited to, addition of terminalamino group(s) and the use of modified internucleotide linkages such as,for example, phosphorothioates, phosphoramidates, and O-methyl ribose ordeoxyribose residues.

Accordingly, embodiments of the present invention may use a donortemplate for HDR that is DNA or RNA, single-stranded and/ordouble-stranded and can be introduced into a cell in linear or circularform.

A donor sequence may be an oligonucleotide and be used for targetedalteration of an endogenous sequence. The oligonucleotide may beintroduced to the cell on a vector, may be electroporated into the cell,or may be introduced via other methods known in the art. Theoligonucleotide can be used to insert a sequence with a desired purposeinto an endogenous locus (e.g. a splice acceptor sequence to preventexpression of a coding exon).

A polynucleotide can be introduced into a cell as part of a vectormolecule having additional sequences such as, for example, replicationorigins, promoters and genes encoding antibiotic resistance. Moreover,donor polynucleotides can be introduced as naked nucleic acid, asnucleic acid complexed with an agent such as a liposome or poloxamer, orcan be delivered by viruses (e.g., adenovirus, AAV, herpesvirus,retrovirus, lentivirus and integrase defective lentivirus (IDLV)).

The donor molecule may be inserted into an endogenous gene such thatall, some or none of the endogenous gene is expressed.

Furthermore, although not required for expression, an exogenous sequenceof a template may also include transcriptional or translationalregulatory sequences, for example, splice donor or splice acceptorsites.

As used herein, the term “modified cells” refers to cells in which adouble strand break is affected by a complex of an RNA molecule and theCRISPR nuclease as a result of hybridization with the target sequence,i.e. on-target hybridization. The term “modified cells” may furtherencompass cells in which a repair or correction of a mutation wasaffected following the double strand break.

This invention provides a modified cell or cells obtained by use of anyof the methods described herein. In an embodiment these modified cell orcells are capable of giving rise to progeny cells. In an embodimentthese modified cell or cells are capable of giving rise to progeny cellsafter engraftment. As a non-limiting example, the modified cells may behematopoietic stem cell (HSC), or any cell suitable for an allogeniccell transplant or autologous cell transplant.

This invention also provides a composition comprising these modifiedcells and a pharmaceutically acceptable carrier. Also provided is an invitro or ex vivo method of preparing this, comprising mixing the cellswith the pharmaceutically acceptable carrier.

As used herein, the term “targeting sequence” or “targeting molecule”refers a nucleotide sequence or molecule comprising a nucleotidesequence that is capable of hybridizing to a specific target sequence,e.g., the targeting sequence has a nucleotide sequence which is at leastpartially complementary to the sequence being targeted along the lengthof the targeting sequence. The targeting sequence or targeting moleculemay be part of an RNA molecule that can form a complex with a CRISPRnuclease, either alone or in combination with other RNA molecules, withthe targeting sequence serving as the targeting portion of the CRISPRcomplex. When the molecule having the targeting sequence is presentcontemporaneously with the CRISPR molecule, the RNA molecule, alone orin combination with an additional one or more RNA molecules (e.g. atracrRNA molecule), is capable of targeting the CRISPR nuclease to thespecific target sequence. As non-limiting example, a guide sequenceportion of a CRISPR RNA molecule or single-guide RNA molecule may serveas a targeting molecule. Each possibility represents a separateembodiment. A targeting sequence can be custom designed to target anydesired sequence.

The term “targets” as used herein, refers to preferentially hybridizinga targeting sequence of a targeting molecule to a nucleic acid having atargeted nucleotide sequence. It is understood that the term “targets”encompasses variable hybridization efficiencies, such that there ispreferential targeting of the nucleic acid having the targetednucleotide sequence, but unintentional off-target hybridization inaddition to on-target hybridization might also occur. It is understoodthat where an RNA molecule targets a sequence, a complex of the RNAmolecule and a CRISPR nuclease molecule targets the sequence fornuclease activity.

The “guide sequence portion” of an RNA molecule refers to a nucleotidesequence that is capable of hybridizing to a specific target DNAsequence, e.g., the guide sequence portion has a nucleotide sequencewhich is partially or fully complementary to the DNA sequence beingtargeted along the length of the guide sequence portion. In someembodiments, the guide sequence portion is 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45, 46, 47, 48, 49 or 50 nucleotides in length, orapproximately 17-50, 17-49, 17-48, 17-47, 17-46, 17-45, 17-44, 17-43,17-42, 17-41, 17-40, 17-39, 17-38, 17-37, 17-36, 17-35, 17-34, 17-33,17-31, 17-30, 17-29, 17-28, 17-27, 17-26, 17-25, 17-24, 17-22, 17-21,18-25, 18-24, 18-23, 18-22, 18-21, 19-25, 19-24, 19-23, 19-22, 19-21,19-20, 20-22, 18-20, 20-21, 21-22, or 17-20 nucleotides in length. Theentire length of the guide sequence portion is fully complementary tothe DNA sequence being targeted along the length of the guide sequenceportion. The guide sequence portion may be part of an RNA molecule thatcan form a complex with a CRISPR nuclease with the guide sequenceportion serving as the DNA targeting portion of the CRISPR complex. Whenthe DNA molecule having the guide sequence portion is presentcontemporaneously with the CRISPR molecule the RNA molecule is capableof targeting the CRISPR nuclease to the specific target DNA sequence.Each possibility represents a separate embodiment. An RNA molecule canbe custom designed to target any desired sequence. Accordingly, amolecule comprising a “guide sequence portion” is a type of targetingmolecule. In some embodiments, the guide sequence portion comprises asequence that is the same as, or differs by no more than 1, 2, 3, 4, or5 nucleotides from, a guide sequence portion described herein, e.g., aguide sequence set forth in any of SEQ ID NOs: 1-20640. Each possibilityrepresents a separate embodiment. In some of these embodiments, theguide sequence portion is fully complementary to the target sequence,and comprises a sequence that is the same as a sequence set forth in anyof SEQ ID NOs: 1-20640. Throughout this application, the terms “guidemolecule,” “RNA guide molecule,” “guide RNA molecule,” and “gRNAmolecule” are synonymous with a molecule comprising a guide sequenceportion.

The term “non-discriminatory” as used herein refers to a guide sequenceportion of an RNA molecule that targets a specific DNA sequence that iscommon both a mutant and functional allele of a gene.

In embodiments of the present invention, an RNA molecule comprises aguide sequence portion having 17-50 contiguous nucleotides containingnucleotides in the sequence set forth in any one of SEQ ID NOs: 1-20640.

The RNA molecule and or the guide sequence portion of the RNA moleculemay contain modified nucleotides. Exemplary modifications to nucleotides/ polynucleotides may be synthetic and encompass polynucleotides whichcontain nucleotides comprising bases other than the naturally occurringadenine, cytosine, thymine, uracil, or guanine bases. Modifications topolynucleotides include polynucleotides which contain synthetic,non-naturally occurring nucleosides e.g., locked nucleic acids.Modifications to polynucleotides may be utilized to increase or decreasestability of an RNA. An example of a modified polynucleotide is an mRNAcontaining 1-methyl pseudo-uridine. For examples of modifiedpolynucleotides and their uses, see U.S. Pat. 8,278,036, PCTInternational Publication No. WO/2015/006747, and Weissman and Kariko(2015), hereby incorporated by reference.

As used herein, “contiguous nucleotides” set forth in a SEQ ID NO refersto nucleotides in a sequence of nucleotides in the order set forth inthe SEQ ID NO without any intervening nucleotides.

In embodiments of the present invention, the guide sequence portion maybe 25 nucleotides in length and contain 20-22 contiguous nucleotides inthe sequence set forth in any one of SEQ ID NOs: 1-20640. In embodimentsof the present invention, the guide sequence portion may be less than 22nucleotides in length. For example, in embodiments of the presentinvention the guide sequence portion may be 17, 18, 19, 20, or 21nucleotides in length. In such embodiments the guide sequence portionmay consist of 17, 18, 19, 20, or 21 nucleotides, respectively, in thesequence of 17-22 contiguous nucleotides set forth in any one of SEQ IDNOs: 1-20640. For example, a guide sequence portion having 17nucleotides in the sequence of 17 contiguous nucleotides set forth inSEQ ID NO: 20641 may consist of any one of the following nucleotidesequences (nucleotides excluded from the contiguous sequence are markedin strike-through):

In embodiments of the present invention, the guide sequence portion maybe greater than 20 nucleotides in length. For example, in embodiments ofthe present invention the guide sequence portion may be 21, 22, 23, 24or 25 nucleotides in length. In such embodiments the guide sequenceportion comprises 17-50 nucleotides containing the sequence of 20, 21 or22 contiguous nucleotides set forth in any one of SEQ ID NOs: 1-20640and additional nucleotides fully complimentary to a nucleotide orsequence of nucleotides adjacent to the 3′ end of the target sequence,5′ end of the target sequence, or both.

In embodiments of the present invention a CRISPR nuclease and an RNAmolecule comprising a guide sequence portion form a CRISPR complex thatbinds to a target DNA sequence to effect cleavage of the target DNAsequence. CRISPR nucleases, e.g. Cpfl, may form a CRISPR complexcomprising a CRISPR nuclease and RNA molecule without a further tracrRNAmolecule. Alternatively, CRISPR nucleases, e.g. Cas9, may form a CRISPRcomplex between the CRISPR nuclease, an RNA molecule, and a tracrRNAmolecule. A guide sequence portion, which comprises a nucleotidesequence that is capable of hybridizing to a specific target DNAsequence, and a sequence portion that participates in CRIPSR nucleasebinding, e.g. a tracrRNA sequence portion, can be located on the sameRNA molecule. Alternatively, a guide sequence portion may be located onone RNA molecule and a sequence portion that participates in CRIPSRnuclease binding, e.g. a tracrRNA portion, may located on a separate RNAmolecule. A single RNA molecule comprising a guide sequence portion(e.g. a DNA-targeting RNA sequence) and at least one CRISPRprotein-binding RNA sequence portion (e.g. a tracrRNA sequence portion),can form a complex with a CRISPR nuclease and serve as the DNA-targetingmolecule. In some embodiments, a first RNA molecule comprising aDNA-targeting RNA portion, which includes a guide sequence portion, anda second RNA molecule comprising a CRISPR protein-binding RNA sequenceinteract by base pairing to form an RNA complex that targets the CRISPRnuclease to a DNA target site or, alternatively, are fused together toform an RNA molecule that complexes with the CRISPR nuclease and targetsthe CRISPR nuclease to a DNA target site.

In embodiments of the present invention, a RNA molecule comprising aguide sequence portion may further comprise the sequence of a tracrRNAmolecule. Such embodiments may be designed as a synthetic fusion of theguide portion of the RNA molecule and the trans-activating crRNA(tracrRNA). (See Jinek et al., 2012). In such an embodiment, the RNAmolecule is a single guide RNA (sgRNA) molecule. Embodiments of thepresent invention may also form CRISPR complexes utilizing a separatetracrRNA molecule and a separate RNA molecule comprising a guidesequence portion. In such embodiments the tracrRNA molecule mayhybridize with the RNA molecule via basepairing and may be advantageousin certain applications of the invention described herein.

The term “tracr mate sequence” refers to a sequence sufficientlycomplementary to a tracrRNA molecule so as to hybridize to the tracrRNAvia basepairing and promote the formation of a CRISPR complex. (See U.S.Pat. No. 8,906,616). In embodiments of the present invention, the RNAmolecule may further comprise a portion having a tracr mate sequence.

A “gene,” for the purposes of the present disclosure, includes a DNAregion encoding a gene product, as well as all DNA regions whichregulate the production of the gene product, whether or not suchregulatory sequences are adjacent to coding and/or transcribedsequences. Accordingly, a gene includes, but is not necessarily limitedto, promoter sequences, terminators, translational regulatory sequencessuch as ribosome binding sites and internal ribosome entry sites,enhancers, silencers, insulators, boundary elements, replicationorigins, matrix attachment sites and locus control regions.

“Eukaryotic” cells include, but are not limited to, fungal cells (suchas yeast), plant cells, animal cells, mammalian cells and human cells.

The term “nuclease” as used herein refers to an enzyme capable ofcleaving the phosphodiester bonds between the nucleotide subunits ofnucleic acid. A nuclease may be isolated or derived from a naturalsource. The natural source may be any living organism. Alternatively, anuclease may be a modified or a synthetic protein which retains thephosphodiester bond cleaving activity. Gene modification can be achievedusing a nuclease, for example a CRISPR nuclease.

As used herein, the term “HSC” refers to both hematopoietic stem cellsand hematopoietic stem progenitor cells. Non-limiting examples of stemcells include bone marrow cells, myeloid progenitor cells, a multipotentprogenitor cells, a lineage restricted progenitor cells.

As used herein, “progenitor cell” refers to a lineage cell that isderived from stem cell and retains mitotic capacity and multipotency(e.g., can differentiate or develop into more than one but not all typesof mature lineage of cell). As used herein “hematopoiesis” or“hemopoiesis” refers to the formation and development of various typesof blood cells (e.g., red blood cells, megakaryocytes, myeloid cells(e.g., monocytes, macrophages and neutrophil), and lymphocytes) andother formed elements in the body (e.g., in the bone marrow).

The term “single nucleotide polymorphism (SNP) position”, as usedherein, refers to a position in which a single nucleotide DNA sequencevariation occurs between members of a species, or between pairedchromosomes in an individual. In the case that a SNP position exists atpaired chromosomes in an individual, a SNP on one of the chromosomes isa “heterozygous SNP.” The term SNP position refers to the particularnucleic acid position where a specific variation occurs and encompassesboth a sequence including the variation from the most frequentlyoccurring base at the particular nucleic acid position (also referred toas “SNP” or alternative “ALT”) and a sequence including the mostfrequently occurring base at the particular nucleic acid position (alsoreferred to as reference, or “REF”). Accordingly, the sequence of a SNPposition may reflect a SNP (i.e. an alternative sequence variantrelative to a consensus reference sequence within a population), or thereference sequence itself.

According to embodiments of the present invention, there is provided amethod for modifying in a cell a mutant allele of the sterile alphamotif domain containing 9 (SAMD9) gene having a mutation associated withMIRAGE syndrome, the method comprising introducing to the cell acomposition comprising:

-   at least one CRISPR nuclease or a sequence encoding a CRISPR    nuclease; and-   a first RNA molecule comprising a guide sequence portion having    17-50 nucleotides or a nucleotide sequence encoding the same,

wherein a complex of the CRISPR nuclease and the first RNA moleculeaffects a double strand break in the mutant allele of the SAMD9 gene.

In some embodiments, the first RNA molecule targets the CRISPR nucleaseto the mutation associated with MIRAGE syndrome.

In some embodiments, the mutation associated with MIRAGE syndrome is anyone of 7:93101391_C_G, 7:93101435_G_A, 7:93101512_C_T, 7:93101540_C_A,7:93101615_T_C, 7:93101761_AGTT_A, 7:93101900_G_A, 7:93102220_C_T,7:93102221_G_A, 7:93102242_G_T, 7:93102259_G_A, 7:93102368_T_C,7:93102514_G_A, 7:93102593_G_A, 7:93102692_C_G, 7:93102717_G_T,7:93103150_AT_GA, 7:93103151_T_C, 7:93103153_C_T, 7:93103178_C_T,7:93103253_C_A, 7:93103393_C_T, 7:93103588_C_CT, 7:93103598_T_A,7:93103628_G_A, 7:93103679_C_T, 7:93103765_G_A, 7:93103772_G_T,7:93103793_C_T, 7:93103851_G_T, 7:93103900_A_G, 7:93103916_T_C,7:93103933_G_T, 7:93103938_GT_G, 7:93104044_C_T, 7:93104176_A_G,7:93104296_ATT_A, 7:93104449_T_A, 7:93104694_TAC_GCA, 7:93104695_AC_GA,7:93104722_C_T, 7:93105043_A_G, 7:93105103_A_G, 7:93105122_G_A,7:93105295_A_G, 7:93105436_C_T, 7:93105485_T_G, 7:93105638_G_A,7:93105781_C_T, 7:93105965_CT_C, 7:93106002_GT_G, 7:93106003_T_A, and7:93106096_A_G.

In some embodiments, the guide sequence portion of the first RNAmolecule comprises 17-50 contiguous nucleotides containing nucleotidesin the sequence set forth in any one of SEQ ID NOs: 1-20640 that targetsa mutation associated with MIRAGE syndrome.

In some embodiments, the method further comprises introduction of adonor molecule for alteration of the SAMD9 mutant allele. In someembodiments, the donor molecule encodes a synthetic splice site (e.g. asplice acceptor or splice donor site) for insertion into the SAMD9mutant allele.

In some embodiments, the first RNA molecule targets the CRISPR nucleaseto a SNP position of the mutant allele.

In some embodiments, the SNP position is any one of rs201891812,rs73216083, rs542330750, rs7798225, rs10953089, rs10953090, rs10277338,rs71562815, rs12333976, rs3839837, rs10279499, rs78564070, rs6965201,rs6969691, rs2374627, rs12668221, rs28673511, rs10229795, rs7785869,rs67885698, rs6957832 and rs12704664.

In some embodiments, the guide sequence portion of the first RNAmolecule comprises 17-50 contiguous nucleotides containing nucleotidesin the sequence set forth in any one of SEQ ID NOs: 1-20640 that targetsa SNP position of the mutant allele.

In some embodiments, the SNP position is in an exon of the SAMD9 mutantallele.

In some embodiments, the SNP position contains a heterozygous SNP.

In some embodiments, the method further comprises introducing to thecell a second RNA molecule comprising a guide sequence portion having17-50 nucleotides or a nucleotide sequence encoding the same, wherein acomplex of the second RNA molecule and a CRISPR nuclease affects asecond double strand break in the SAMD9 gene.

In some embodiments, the guide sequence portion of the second RNAmolecule comprises 17-50 contiguous nucleotides containing nucleotidesin the sequence set forth in any one of SEQ ID NOs: 1-20640 other thanthe sequence of the first RNA molecule.

In some embodiments, the second RNA molecule comprises anon-discriminatory guide portion that targets both functional andmutated SAMD9 alleles.

In some embodiments, the second RNA molecule comprises anon-discriminatory guide portion that targets any one of a SAMD9untranslated region (UTR), an intergenic region upstream of SAMD9, anintergenic region downstream of SAMD9, or Intron 2 of SAMD9.

In some embodiments, the second RNA molecule comprises anon-discriminatory guide portion that targets a sequence that is locatedwithin a genomic range selected from any one of 7:93100828 to7:93101327, 7:93099521 to 7:93100020, 7:93099413 to 7:93099913, or7:93106106 to 7:93106605.

In some embodiments, the second RNA molecule comprises anon-discriminatory guide portion that targets a sequence that is locatedup to 500 base pairs from the sequence targeted by the first RNAmolecule.

In some embodiments, a portion of an exon is excised from the mutantallele of the SAMD9 gene.

In some embodiments, the first RNA molecule targets a SNP position inthe 3′ UTR of the mutated allele, and the second RNA molecule comprisesa non-discriminatory guide portion that targets downstream of apolyadenylation signal sequence that is common to both a functionalallele and the mutant allele of the SAMD9 gene.

In some embodiments, the first RNA molecule targets a SNP positiondownstream of a polyadenylation signal of the mutated allele, and thesecond RNA molecule comprises a non-discriminatory guide portion thattargets a sequence upstream of a polyadenylation signal that is commonto both a functional allele and the mutant allele of the SAMD9 gene.

In some embodiments, the polyadenylation signal is excised from themutant allele of the SAMD9 gene.

According to embodiments of the present invention, there is provided amodified cell obtained by the method of any one of the embodimentspresented herein.

According to embodiments of the present invention, there is provided afirst RNA molecule comprising a guide sequence portion having 17-50contiguous nucleotides containing nucleotides in the sequence set forthin any one of SEQ ID NOs: 1-20640.

According to embodiments of the present invention, there is provided acomposition comprising the first RNA molecule and at least one CRISPRnuclease.

In some embodiments, the composition further comprises a second RNAmolecule comprising a guide sequence portion having 17-50 contiguousnucleotides, wherein the second RNA molecule targets a SAMD9 allele, andwherein the guide sequence portion of the second RNA molecule is adifferent sequence from the sequence of the guide sequence portion ofthe first RNA molecule.

In some embodiments, the guide sequence portion of the second RNAmolecule comprises 17-50 contiguous nucleotides containing nucleotidesin the sequence set forth in any one of SEQ ID NOs: 1-20640 other thanthe sequence of the first RNA molecule.

According to embodiments of the present invention, there is provided amethod for inactivating a mutant SAMD9 allele in a cell, the methodcomprising delivering to the cell the composition of any one of theembodiments presented herein.

According to embodiments of the present invention, there is provided amethod for treating MIRAGE syndrome, the method comprising delivering toa cell of a subject having MIRAGE syndrome the composition of any one ofthe embodiments presented herein.

According to embodiments of the present invention, there is provided useof any one of the compositions presented herein for inactivating amutant SAMD9 allele in a cell, comprising delivering to the cell thecomposition of any one of the embodiments presented herein.

According to embodiments of the present invention, there is provided amedicament comprising the composition of any one of the embodimentspresented herein for use in inactivating a mutant SAMD9 allele in acell, wherein the medicament is administered by delivering to the cellthe composition of any one of the embodiments presented herein.

According to embodiments of the present invention, there is provided useof the composition of any one of the embodiments presented herein fortreating ameliorating or preventing MIRAGE syndrome, comprisingdelivering to a cell of a subject having or at risk of having MIRAGEsyndrome the composition of any one of the embodiments presented herein.

According to embodiments of the present invention, there is provided amedicament comprising the composition of any one of the embodimentspresented herein for use in treating ameliorating or preventing MIRAGEsyndrome, wherein the medicament is administered by delivering to a cellof a subject having or at risk of having MIRAGE syndrome the compositionof any one of the embodiments presented herein.

According to embodiments of the present invention, there is provided akit for inactivating a mutant SAMD9 allele in a cell, comprising an RNAmolecule of any one of the embodiments presented herein, a CRISPRnuclease, and/or a tracrRNA molecule; and instructions for deliveringthe RNA molecule; CRISPR nuclease, and/or the tracrRNA to the cell.

According to embodiments of the present invention, there is provided akit for treating MIRAGE syndrome in a subject, comprising an RNAmolecule of any one of the embodiments presented herein, a CRISPRnuclease, and/or a tracrRNA molecule; and instructions for deliveringthe RNA molecule; CRISPR nuclease, and/or the tracrRNA to a cell of asubject having or at risk of having MIRAGE syndrome.

According to embodiments of the present invention, there is provided agene editing composition comprising an RNA molecule comprising a guidesequence portion having 17-50 contiguous nucleotides containingnucleotides in the sequence set forth in any one of SEQ ID NOs: 1-20640.In some embodiments, the RNA molecule further comprises a portion havinga sequence which binds to a CRISPR nuclease. In some embodiments, thesequence which binds to a CRISPR nuclease is a tracrRNA sequence.

In some embodiments, the RNA molecule further comprises a portion havinga tracr mate sequence.

In some embodiments, the RNA molecule may further comprise one or morelinker portions.

According to embodiments of the present invention, an RNA molecule maybe up to 1000, 900, 800, 700, 600, 500, 450, 400, 350, 300, 290, 280,270, 260, 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140,130, 120, 110, or 100 nucleotides in length. Each possibility representsa separate embodiment. In embodiments of the present invention, the RNAmolecule may be 17 up to 300 nucleotides in length, 100 up to 300nucleotides in length, 150 up to 300 nucleotides in length, 100 up to500 nucleotides in length, 100 up to 400 nucleotides in length, 200 upto 300 nucleotides in length, 100 to 200 nucleotides in length, or 150up to 250 nucleotides in length. Each possibility represents a separateembodiment.

According to some embodiments of the present invention, the compositionfurther comprises a tracrRNA molecule.

The present disclosure provides a method for utilizing at least onenaturally occurring nucleotide difference or polymorphism (e.g., singlenucleotide polymorphism (SNP)) for distinguishing/discriminating betweentwo alleles of a gene, one allele bearing a mutation such that itencodes a mutated protein causing a disease phenotype (“mutated allele”)and a particular sequence in a SNP position (SNP/REF), and the otherallele encoding for a functional protein (“functional allele”). Themethod further comprises the step of knocking out expression of themutated protein and allowing expression of the functional protein. Insome embodiments, the method is for treating, ameliorating, orpreventing a dominant negative genetic disorder.

According to some embodiments of the present invention, there isprovided a method for inactivating a mutant SAMD9 allele in a cell, themethod comprising delivering to the cell a composition comprising an RNAmolecule comprising a guide sequence portion having 17-50 contiguousnucleotides containing nucleotides in the sequence set forth in any oneof SEQ ID NOs: 1-20640 and a CRISPR nuclease.

According to some embodiments of the present invention, there isprovided a method for treating MIRAGE syndrome, the method comprisingdelivering to a cell of a subject having MIRAGE syndrome a compositioncomprising an RNA molecule comprising a guide sequence portion having17-50 contiguous nucleotides containing nucleotides in the sequence setforth in any one of SEQ ID NOs: 1-20640 and a CRISPR nuclease.

According to embodiments of the present invention, the compositioncomprises a second RNA molecule comprising a guide sequence portionhaving 17-50 contiguous nucleotides containing nucleotides in thesequence set forth in any one of SEQ ID NOs: 1-20640. In someembodiments, the 17-50 nucleotides of the guide sequence portion of thesecond RNA molecule are in a different sequence from the sequence of theguide sequence portion of the first RNA molecule.

According to embodiments of the present invention, at least one CRISPRnuclease and the RNA molecule or RNA molecules are delivered to thesubject and/or cells substantially at the same time or at differenttimes.

In some embodiments, a tracrRNA molecule is delivered to the subjectand/or cells substantially at the same time or at different times as theCRISPR nuclease and RNA molecule or RNA molecules.

According to embodiments of the present invention, the first RNAmolecule targets a SNP or disease-causing mutation in the exon orpromoter of a mutated allele, and the second RNA molecule targets a SNPin an exon of the mutated allele, a SNP in an intron, or a sequencepresent in both the mutated or functional allele.

According to embodiments of the present invention, the first RNAmolecule or the first and the second RNA molecules target a SNP in thepromoter region, the start codon, or an untranslated region (UTR) of amutated allele.

According to embodiments of the present invention, the first RNAmolecule or the first and the second RNA molecules targets at least aportion of the promoter and/or the start codon and/or a portion of a UTRof a mutated allele.

According to embodiments of the present invention, the first RNAmolecule targets a portion of the promoter, a first SNP in the promoter,or a SNP upstream to the promoter of a mutated allele and the second RNAmolecule is targets a second SNP, which is downstream of the first SNP,and is in the promoter, in a UTR, or in an intron or in an exon of amutated allele.

According to embodiments of the present invention, the first RNAmolecule targets a SNP in the promoter, upstream of the promoter, or aUTR of a mutated allele and the second RNA molecule is designed totarget a sequence which is present in an intron of both the mutatedallele and the functional allele.

According to embodiments of the present invention, the first RNAmolecule targets a SNP in an intron of a mutated allele, and wherein thesecond RNA molecule targets a SNP in an intron of the mutated allele, ora sequence in an intron present in both the mutated and functionalallele.

According to embodiments of the present invention, the first RNAmolecule targets a sequence upstream of the promotor which is present inboth a mutated and functional allele and the second RNA molecule targetsa SNP or disease-causing mutation in any location of the gene.

According to embodiments of the present invention, there is provided amethod comprising removing an exon containing a disease-causing mutationfrom a mutated allele, wherein the first RNA molecule or the first andthe second RNA molecules target regions flanking an entire exon or aportion of the exon.

According to embodiments of the present invention, there is provided amethod comprising removing an exon or a portion thereof from a mutantSAMD9 allele, the entire open reading frame of a mutant SAMD9 allele, orremoving the entire mutant SAMD9 allele.

According to embodiments of the present invention, the first RNAmolecule targets a SNP or disease-causing mutation in an exon orpromoter of a mutated allele, and wherein the second RNA moleculetargets a SNP in the same exon of the mutated allele, a SNP in anintron, or a sequence in an intron present in both the mutated andfunctional allele.

According to embodiments of the present invention, the first RNAmolecule or the first and the second RNA molecules target an alternativesplicing signal sequence between an exon and an intron of a mutant SAMD9allele.

According to embodiments of the present invention, the second RNAmolecule is non-discriminatory targets a sequence present in both amutated allele and a functional allele.

The compositions and methods of the present disclosure may be utilizedfor treating, preventing, ameliorating, or slowing progression of anautosomal dominant genetic disorder, such as MIRAGE syndrome.

In some embodiments, a mutated allele is deactivated by delivering to acell an RNA molecule which targets a SNP in the promoter region, thestart codon, or an untranslated region (UTR) of the mutated allele.

In some embodiments, a mutated allele is inactivated by removing atleast a portion of the promoter, and/or removing the start codon, and/ora portion of the UTR, and/or a polyadenylation signal. In suchembodiments one RNA molecule may be designed for targeting a first SNPin the promoter or upstream to the promoter and another RNA molecule isdesigned to target a second SNP, which is downstream of the first SNP,and is in the promoter, in the UTR, in an intron, or in an exon.Alternatively, one RNA molecule may be designed for targeting a SNP inthe promoter, upstream of the promoter, or the UTR, and another RNAmolecule is designed to target a sequence which is present in an intronof both the mutated allele and the functional allele. Alternatively, oneRNA molecule may be designed for targeting a sequence upstream of thepromotor which is present in both the mutated and functional allele andthe other guide is designed to target a SNP or disease-causing mutationin any location of the gene e.g., in an exon, intron, UTR, or downstreamof the promoter.

In some embodiments, the method of deactivating a mutated allelecomprises an exon skipping step comprising removing an exon containing adisease-causing mutation from the mutated allele. Removing an exoncontaining a disease-causing mutation in the mutated allele requires twoRNA molecules which target regions flanking the entire exon or a portionof the exon. Removal of an exon containing the disease-causing mutationmay be designed to eliminate the disease-causing action of the proteinwhile allowing for expression of the remaining protein product whichretains some or all of the wild-type activity. The entire open readingframe or the entire gene can be excised using two RNA molecules flankingthe region desired to be excised.

In some embodiments, the method of deactivating a mutated allelecomprises delivering two RNA molecules to a cell, wherein one RNAmolecule targets a SNP or disease-causing mutation in an exon orpromoter of the mutated allele, and wherein the other RNA moleculetargets a SNP in the same of the mutated allele, a SNP in an intron, ora sequence in an intron present in both the mutated or functionalallele.

Any one of, or combination of, the above-mentioned strategies fordeactivating a mutant allele may be used in the context of theinvention.

In embodiments of the present invention, an RNA molecule is used todirect a CRISPR nuclease to an exon or a splice site of a mutated allelein order to create a double-stranded break (DSB), leading to insertionor deletion of nucleotides by inducing an error-prone non-homologousend-joining (NHEJ) mechanism and formation of a frameshift mutation inthe mutated allele. The frameshift mutation may result in, for example,inactivation or knockout of the mutated allele by generation of an earlystop codon in the mutated allele and to generation of a truncatedprotein or to nonsense-mediated mRNA decay of the transcript of themutant allele. In further embodiments, one RNA molecule is used todirect a CRISPR nuclease to a promotor of a mutated allele.

In some embodiments, the method of deactivating a mutated allele furthercomprises enhancing activity of the functional protein such as byproviding a protein/peptide, a nucleic acid encoding a protein/peptide,or a small molecule such as a chemical compound, capable ofactivating/enhancing activity of the functional protein.

According to some embodiments, the present disclosure provides an RNAsequence (also referred to as an ‘RNA molecule’) which binds to orassociates with and/or directs an RNA-guided DNA nuclease e.g., a CRISPRnuclease, to a target sequence comprising at least one nucleotide whichdiffers between a mutated allele and a functional allele (e.g., SNP) ofa gene of interest (i.e., a sequence of the mutated allele which is notpresent in the functional allele).

In some embodiments, the method comprises contacting a mutated allele ofa gene of interest with an allele-specific RNA molecule and a CRISPRnuclease e.g., a Cas9 protein, wherein the allele-specific RNA moleculeand the CRISPR nuclease associate with a nucleotide sequence of themutated allele of the gene of interest which differs by at least onenucleotide from a nucleotide sequence of a functional allele of the geneof interest, thereby modifying or knocking-out the mutated allele.

In some embodiments, the allele-specific RNA molecule and a CRISPRnuclease is introduced to a cell encoding the gene of interest. In someembodiments, the cell encoding the gene of interest is in a mammaliansubject. In some embodiments, the cell encoding the gene of interest isin a plant.

In some embodiments, the mutated allele is an allele of SAMD9 gene. Insome embodiments, the RNA molecule targets a SNP which co-exists with oris genetically linked to the mutated sequence associated with MIRAGEsyndrome genetic disorder. In some embodiments, the RNA molecule targetsa SNP which is highly prevalent in the population and exists in themutated allele having the mutated sequence associated with MIRAGEsyndrome genetic disorder and not in the functional allele of anindividual subject to be treated. In some embodiments, a disease-causingmutation within a mutated SAMD9 allele is targeted.

In some embodiments, the SNP is within an exon of the gene of interest.In such embodiments, a guide sequence portion of an RNA molecule isdesigned to associate with a sequence of an exon of the gene ofinterest.

In some embodiments, SNP is within an intron or the exon of the gene ofinterest. In some embodiments, the SNP is in close proximity to thesplice site between an intron and an exon. In some embodiments, theclose proximity to a splice site is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides upstream or downstreamto the splice site. Each possibility represents a separate embodiment ofthe present invention. In such embodiments, a guide sequence portion ofan RNA molecule may be designed to associate with a sequence of the geneof interest which comprises the splice site.

In some embodiments, the method is utilized for treating a subjecthaving a disease phenotype resulting from the heterozygote SAMD9 gene.In such embodiments, the method results in improvement, amelioration orprevention of the disease phenotype.

Embodiments of compositions described herein include at least one CRISPRnuclease, RNA molecule(s), and a tracrRNA molecule, being effective in asubject or cells at the same time. The at least one CRISPR nuclease, RNAmolecule(s), and tracrRNA may be delivered substantially at the sametime or can be delivered at different times but have effect at the sametime. For example, this includes delivering the CRISPR nuclease to thesubject or cells before the RNA molecule and/or tracrRNA issubstantially extant in the subject or cells.

In some embodiments, the cell is a stem cell. In some embodiments, thecell is an embryonic stem cell. In some embodiments, the stem cell is ahematopoietic stem/progenitor cell (HSC).

Dominant Genetic Disorders

One of skill in the art will appreciate that all subjects with any typeof heterozygote genetic disorder (e.g., dominant genetic disorder) maybe subjected to the methods described herein. In one embodiment, thepresent invention may be used to target a gene involved in, associatedwith, or causative of dominant genetic disorders such as, for example,MIRAGE syndrome. In some embodiments, the dominant genetic disorder isMIRAGE syndrome. In some embodiments, the target gene is the SAMD9 gene(Entrez Gene, gene ID No: 54809). Non-limiting examples of mutationspreviously characterized as gain of function mutations associated withMIRAGE syndrome phenotype include: 7:93101391_C_G, 7:93101435_G_A,7:93101512_C_T, 7:93101540_C_A, 7:93101615_T_C, 7:93101761_AGTT_A,7:93101900_G_A, 7:93102220_C_T, 7:93102221_G_A, 7:93102242_G_T,7:93102259_G_A, 7:93102368_T_C, 7:93102514_G_A, 7:93102593_G_A,7:93102692_C_G, 7:93102717_G_T, 7:93103150_AT_GA, 7:93103151_T_C,7:93103153_C_T, 7:93103178_C_T, 7:93103253_C_A, 7:93103393_C_T,7:93103588_C_CT, 7:93103598_T_A, 7:93103628_G_A, 7:93103679_C_T,7:93103765_G_A, 7:93103772_G_T, 7:93103793_C_T, 7:93103851_G_T,7:93103900_A_G, 7:93103916_T_C, 7:93103933_G_T, 7:93103938_GT_G,7:93104044_C_T, 7:93104176_A_G, 7:93104296_ATT_A, 7:93104449_T_A,7:93104694_TAC_GCA, 7:93104695_AC_GA, 7:93104722_C_T, 7:93105043_A_G,7:93105103_A_G, 7:93105122_G_A, 7:93105295_A_G, 7:93105436_C_T,7:93105485_T_G, 7:93105638_G_A, 7:93105781_C_T, 7:93105965_CT_C,7:93106002_GT_G, 7:93106003_T_A, and 7:93106096_A_G.

SAMD9 editing strategies include, but are not limited to, (1)truncation; (2) inhibiting expression of a mutated SAMD9 allele; (3)excision of the mutated coding exon or polyadenylation signal; and (4)targeting a SAMD9 mutation to induce a frameshift; and (5) inducinghomology directed repair (HDR) to introduce a synthetic splice siteupstream of the coding exon with a donor molecule.

Truncation can be achieved by several approaches. For example, excisionmay be achieved by targeting the mutant SAMD9 allele with two differentRNA molecules, e.g. single guide RNA molecules or “sgRNAs”. At least oneRNA molecule is preferably allele-specific. Alternatively, truncationmay also be achieved by targeting a SNP within the coding exon of amutant SAMD9 allele using a single guide RNA molecule.

In another approach, truncation can be achieved by introducing a spliceacceptor by HDR. A splice acceptor sequence can be introduced using, forexample, a double-stranded donor oligonucleotide (dsODN) template thatwill be introduced in Intron 2 before the coding exon.

In another editing strategy, expression of a mutated SAMD9 allele may beinhibited. This can be achieved by excising the polyadenylation signalin the 3′UTR region, which leads to an unstable transcript.

According to embodiments of the present invention, there is provided anRNA molecule comprising a guide sequence portion (e.g., a targetingsequence) comprising a nucleotide sequence that is fully or partiallycomplementary to a target sequence in a SNP position (REF/SNP sequence)located in or near a mutated allele of the SAMD9 gene. In someembodiments, the guide sequence portion of the RNA molecule consists of16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or more than 26 nucleotides.In such embodiments, the guide sequence portion comprises a sequencethat is the same as or differs by no more than 1, 2, or 3 nucleotidesfrom a sequence set forth in Table 1. Each possibility represents aseparate embodiment. In some embodiments the guide sequence portion isconfigured to target a CRISPR nuclease to a target sequence and providea cleavage event, by a CRISPR nuclease complexed therewith, selectedfrom a double-strand break and a single-strand break within 500, 400,300, 200, 100, 50, 25, or 10 nucleotides of a SAMD9 target site. In someembodiments, the cleavage event enables non-sense mediated decay of theSAMD9 gene. In some embodiments, the RNA molecule is a guide RNAmolecule such as a crRNA molecule or a single guide RNA molecule.

In some embodiments, the target sequence of a mutated allele of SAMD9gene is altered (e.g., by introduction of an NHEJ-mediated indel (e.g.,insertion or deletion), and results in reduction or elimination ofexpression of the gene product encoded by the mutant allele of SAMD9gene. In some embodiments, the reduction or elimination of expression isdue to non-sense mediated mRNA decay such as due to immature stop codon.In some embodiments, the reduction or elimination of expression is dueto expression of a truncated form of the SAMD9 gene product. In someembodiments, the guide sequence portion is complementary to a targetsequence in a SNP position located in the coding exon (Exon 3) or from7, 30, or 50 base pairs upstream to 7, 30, or 50 base pairs downstreamof the coding exon (Exon 3) of the mutated allele of the SAMD9 gene.Each possibility represents a separate embodiment. In such embodiments,the guide sequence portion comprises a sequence that targets a SNPposition selected from: rs10279499, rs78564070, rs6965201, or rs6969691.In such embodiments, the guide sequence portion comprises a sequencethat is the same as or differs by no more than 1, 2, or 3 nucleotidesfrom a sequence selected from any of SEQ ID NOs: 9909-10964, 5744, 5746,5765, 5772, 5776, 5780, 5786, 5789, 5791, 5796, 5798, 5815, 5818, 5825,5840, 5843, 5845, 5852, 5854, 5869, 5872, 5880, 5891, 5899, 6678-6679,6681, 6688, 6692, 6696, 6710, 6714, or 6722, or from a sequence setforth in any of the SEQ ID NOs listed as targeting rs10279499,rs78564070, rs6965201, or rs6969691 in Table 1.

In some embodiments, the guide sequence portion is complementary totarget a pathogenic mutation located in the coding exon (Exon 3) of themutated allele of the SAMD9 gene to reduce or eliminate expression ofthe mutated SAMD9 allele. In such embodiments, the guide sequenceportion comprises a sequence that targets a mutation selected from:7:93101391_C_G, 7:93101435_G_A, 7:93101512_C_T, 7:93101540_C_A,7:93101615_T_C, 7:93101761_AGTT_A, 7:93101900_G_A, 7:93102220_C_T,7:93102221_G_A, 7:93102242_G_T, 7:93102259_G_A, 7:93102368_T_C,7:93102514_G_A, 7:93102593_G_A, 7:93102692_C_G, 7:93102717_G_T,7:93103150_AT_GA, 7:93103151_T_C, 7:93103153_C_T, 7:93103178_C_T,7:93103253_C_A, 7:93103393_C_T, 7:93103588_C_CT, 7:93103598_T_A,7:93103628_G_A, 7:93103679_C_T, 7:93103765_G_A, 7:93103772_G_T,7:93103793_C_T, 7:93103851_G_T, 7:93103900_A_G, 7:93103916_T_C,7:93103933_G_T, 7:93103938_GT_G, 7:93104044_C_T, 7:93104176_A _G,7:93104296_ATT_A, 7:93104449_T_A, 7:93104694_TAC_GCA, 7:93104695_AC_GA,7:93104722_C_T, 7:93105043_A _G, 7:93105103_A_G, 7:93105122_G_A,7:93105295_A_G, 7:93105436_C_T, 7:93105485_T_G, 7:93105638_G_A,7:93105781_C_T, 7:93105965_CT_C, 7:93106002_GT_G, 7:93106003_T_A, and7:93106096_A_G. In some embodiments, the reduction or elimination ofexpression is due to non-sense mediated mRNA decay such as due toimmature stop codon. In some embodiments, the reduction or eliminationof expression is due to expression of a truncated form of the SAMD9 geneproduct of the mutant allele. In some embodiments, a donor HDR isfurther introduced to correct the sequence of the mutant allele of theSAMD9 gene.

In some embodiments, the expression of the coding exon of a mutatedallele of SAMD9 gene is eliminated by introducing a splice acceptordirectly upstream of the coding exon (e.g., to intron 2) of the mutatedallele. In some embodiments, the target sequence is a SNP position inintron 2 of a mutated allele of SAMD9 gene, to which a splice acceptoris introduced such as by HDR following DSB by a RNA targeted DNANuclease, this results in reduction or elimination of expression of thegene product encoded by the mutant allele of SAMD9 gene. In suchembodiments, the SNP position in intron 2 is any one of: rs2374627,rs12668221, rs28673511, rs10229795, rs7785869, rs67885698, rs6957832, orrs12704664. In such embodiments, the first guide sequence portioncomprises a sequence that is the same as or differs by no more than 1,2, or 3 nucleotides from a sequence set forth in any of the SEQ ID NOslisted as targeting rs2374627, rs12668221, rs28673511, rs10229795,rs7785869, rs67885698, rs6957832, or rs12704664 in Table 1. A personskilled in the art will appreciate that many splice acceptor sequencescan be utilized.

In some embodiments, the coding exon of a mutated allele of SAMD9 geneis completely or partially excised to reduce or eliminate expression ofthe mutant allele of the SAMD9 gene. In such embodiments at least twodifferent guide sequence portions are utilized, a first guide sequenceportion is a discriminatory guide targeting only a mutated allele of theSAMD9 gene, and a second guide sequence portion is non-discriminatoryand targets non-coding regions of both alleles of the SAMD9 gene.

In some embodiments, the first guide sequence portion is complementaryto a target sequence in a SNP position located in intron 2 of themutated allele of the SAMD9 gene, and the second guide sequence portionis complementary to a target sequence in the 3′ UTR or in the intergenicregion of the SAMD9 gene. In such embodiments, the SNP position is anyone of rs2374627, rs12668221, rs28673511, rs10229795, rs7785869,rs67885698, rs6957832, or rs12704664. In such embodiments, the firstguide sequence portion comprises a sequence that is the same as ordiffers by no more than 1, 2, or 3 nucleotides from a sequence set forthin any of the SEQ ID NOs listed as targeting rs2374627, rs12668221,rs28673511, rs10229795, rs7785869, rs67885698, rs6957832, or rs12704664in Table 1.

In some embodiments, the first guide sequence portion is complementaryto a target sequence in a SNP position located in intergenic region ofthe mutated allele of the SAMD9 gene, and the second guide sequenceportion is complementary to a target sequence in intron 2 of the SAMD9gene. In such embodiments, the SNP position is any one of: rs71562815,rs12333976, rs3839837, rs201891812, rs73216083, rs542330750, rs7798225,rs10953089, rs10953090, or rs10277338. In such embodiments, the firstguide sequence portion comprises a sequence that is the same as ordiffers by no more than 1, 2, or 3 nucleotides from a sequence set forthin any of the SEQ ID NOs listed as targeting rs71562815, rs12333976,rs3839837, rs201891812, rs73216083, rs542330750, rs7798225, rs10953089,rs10953090, or rs10277338 in Table 1. In such embodiments, the secondguide sequence portion comprises a sequence that is the same as ordiffers by no more than 1, 2, or 3 nucleotides from a sequence set forthin any of SEQ ID Nos: 18323-20640, or from the SEQ ID NOs listed astargeting intron 2 of the SAMD9 gene in Table 1.

In some embodiments, the first guide sequence portion is complementaryto a target sequence in a SNP position located in 3′ UTR of the mutatedallele of the SAMD9 gene, and the second guide sequence portion iscomplementary to a target sequence in intron 2 of the SAMD9 gene. Insuch embodiments, the SNP position in the 3′UTR is any one ofrs71562815, rs12333976, or rs3839837. In such embodiments, the firstguide sequence portion comprises a sequence that is the same as ordiffers by no more than 1, 2, or 3 nucleotides from a sequence set forthin any of SEQ ID Nos: 9471-9908, or from the SEQ ID NOs listed astargeting rs71562815, rs12333976, or rs3839837 in Table 1. In suchembodiments, the second guide sequence portion comprises a sequence thatis the same as or differs by no more than 1, 2, or 3 nucleotides from asequence set forth in any of SEQ ID Nos: 18323-20640.

In some embodiments, the polyadenylation signal (PolyAS) of SAMD9 geneof the mutated allele of the SAMD9 gene is completely or partiallyexcised to destabilize the mutated allele to reduce or eliminateexpression of the mutant allele.

In some embodiments, the first guide sequence portion is complementaryto a target sequence in a SNP position located in 3′ UTR of the mutatedallele of the SAMD9 gene, and the second guide sequence portion iscomplementary to a target sequence in the intergenic region of the SAMD9gene. In such embodiments, the SNP position in the 3′UTR is any one ofrs71562815, rs12333976, or rs3839837. In such embodiments, the firstguide sequence portion comprises a sequence that is the same as ordiffers by no more than 1, 2, or 3 nucleotides from a sequence set forthin any of SEQ ID Nos: 9471-9908, or from the SEQ ID NOs listed astargeting rs71562815, rs12333976, or rs3839837 in Table 1.

In some embodiments, the first guide sequence portion is complementaryto a target sequence in a SNP position located in intergenic region ofthe mutated allele of the SAMD9 gene, and the second guide sequenceportion is complementary to a target sequence in the 3′ UTR of the SAMD9gene. In such embodiments, the SNP position in the intergenic region isany one of rs71562815, rs12333976, rs3839837, rs201891812, rs73216083,rs542330750, rs7798225, rs10953089, rs10953090, or rs10277338. In suchembodiments, the first guide sequence portion comprises a sequence thatis the same as or differs by no more than 1, 2, or 3 nucleotides from asequence set forth in any of the SEQ ID NOs listed as targetingrs71562815, rs12333976, rs3839837, rs201891812, rs73216083, rs542330750,rs7798225, rs10953089, rs10953090, or rs10277338 in Table 1. In suchembodiments, the second guide sequence portion comprises a sequence thatis the same as or differs by no more than 1, 2, or 3 nucleotides from asequence set forth in any of SEQ ID Nos: 12756-17909, or from the SEQ IDNOs listed as targeting the 3′ UTR of the SAMD9 gene in Table 1.

CRISPR Nucleases and PAM Recognition

In some embodiments, the sequence specific nuclease is selected fromCRISPR nucleases, or a functional variant thereof. In some embodiments,the sequence specific nuclease is an RNA guided DNA nuclease. In suchembodiments, the RNA sequence which guides the RNA guided DNA nuclease(e.g., Cpfl) binds to and/or directs the RNA guided DNA nuclease to thesequence comprising at least one nucleotide which differs between amutated allele and its counterpart functional allele (e.g., SNP). Insome embodiments, the CRISPR complex does not further comprise atracrRNA. In a non-limiting example, in which the RNA guided DNAnuclease is a CRISPR protein, the at least one nucleotide which differsbetween the dominant mutated allele and the functional allele may bewithin the PAM site and/or proximal to the PAM site within the regionthat the RNA molecule is designed to hybridize to. A skilled artisanwill appreciate that RNA molecules can be engineered to bind to a targetof choice in a genome by commonly known methods in the art.

The term “PAM” as used herein refers to a nucleotide sequence of atarget DNA located in proximity to the targeted DNA sequence andrecognized by the CRISPR nuclease complex. The PAM sequence may differdepending on the nuclease identity. In addition, there are CRISPRnucleases that can target almost all PAMs. In some embodiments of thepresent invention, a CRISPR system utilizes one or more RNA moleculeshaving a guide sequence portion to direct a CRISPR nuclease to a targetDNA site via Watson-Crick base-pairing between the guide sequenceportion and the protospacer on the target DNA site, which is next to theprotospacer adjacent motif (PAM), which is an additional requirement fortarget recognition. The CRISPR nuclease then mediates cleavage of thetarget DNA site to create a double-stranded break within theprotospacer. In a non-limiting example, a type II CRISPR system utilizesa mature crRNA:tracrRNA complex that directs the CRISPR nuclease, e.g.Cas9 to the target DNA the target DNA via Watson-Crick base-pairingbetween the guide sequence portion of the crRNA and the protospacer onthe target DNA next to the protospacer adjacent motif (PAM). A skilledartisan will appreciate that each of the engineered RNA molecule of thepresent invention is further designed such as to associate with a targetgenomic DNA sequence of interest next to a protospacer adjacent motif(PAM), e.g., a PAM matching the sequence relevant for the type of CRISPRnuclease utilized, such as for a non-limiting example, NGG or NAG,wherein “N” is any nucleobase, for Streptococcus pyogenes Cas9 WT(SpCAS9); NNGRRT for Staphylococcus aureus (SaCas9); NNNVRYM for JejuniCas9 WT; NGAN or NGNG for SpCas9-VQR variant; NGCG for SpCas9-VRERvariant; NGAG for SpCas9-EQR variant; NRRH for SpCas9-NRRH variant,wherein N is any nucleobase, R is A or G and H is A, C, or T; NRTH forSpCas9-NRTH variant, wherein N is any nucleobase, R is A or G and H isA, C, or T; NRCH for SpCas9-NRCH variant, wherein N is any nucleobase, Ris A or G and H is A, C, or T; NG for SpG variant of SpCas9 wherein N isany nucleobase; NG or NA for SpCas9-NG variant of SpCas9 wherein N isany nucleobase; NR or NRN or NYN for SpRY variant of SpCas9, wherein Nis any nucleobase, R is A or G and Y is C or T; NNG for Streptococcuscanis Cas9 variant (ScCas9), wherein N is any nucleobase; NNNRRT forSaKKH-Cas9 variant of Staphylococcus aureus (SaCas9), wherein N is anynucleobase, and R is A or G; NNNNGATT for Neisseria meningitidis(NmCas9), wherein N is any nucleobase; TTN for Alicyclobacillusacidiphilus Cas12b (AacCas12b), wherein N is any nucleobase; or TTTV forCpfl, wherein V is A, C or G. RNA molecules of the present invention areeach designed to form complexes in conjunction with one or moredifferent CRISPR nucleases and designed to target polynucleotidesequences of interest utilizing one or more different PAM sequencesrespective to the CRISPR nuclease utilized.

In some embodiments, an RNA-guided DNA nuclease e.g., a CRISPR nuclease,may be used to cause a DNA break, either double or single-stranded innature, at a desired location in the genome of a cell. The most commonlyused RNA-guided DNA nucleases are derived from CRISPR systems, however,other RNA-guided DNA nucleases are also contemplated for use in thegenome editing compositions and methods described herein. For instance,see U.S. Pat. Publication No. 2015/0211023, incorporated herein byreference.

CRISPR systems that may be used in the practice of the invention varygreatly. CRISPR systems can be a type I, a type II, or a type IIIsystem. Non- limiting examples of suitable CRISPR proteins include Cas3,Cas4, Cas5, Cas5e (or CasD), Cas6, Cas6e, Cas6f, Cas7, Cas8al, Cas8a2,Cas8b, Cas8c, Cas9, Cas10, Cas1 Od, CasF, CasG, CasH, Csy1, Csy2, Csy3,Csel (or CasA), Cse2 (or CasB), Cse3 (or CasE), Cse4 (or CasC), Cscl,Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5,Cmr6, Csbl, Csb2, Csb3,Csxl7, Csxl4, Csxl0, Csxl6, CsaX, Csx3, Cszl,Csxl5, Csf1, Csf2, Csf3, Csf4, and Cul966.

In some embodiments, the RNA-guided DNA nuclease is a CRISPR nucleasederived from a type II CRISPR system (e.g., Cas9). The CRISPR nucleasemay be derived from Streptococcus pyogenes, Streptococcus thermophilus,Streptococcus sp., Staphylococcus aureus, Neisseria meningitidis,Treponema denticola, Nocardiopsis dassonvillei, Streptomycespristinaespiralis, Streptomyces viridochromogenes, Streptomycesviridochromogenes, Streptosporangium roseum, Streptosporangium roseum,Alicyclobacillus acidocaldarius, Bacillus pseudomycoides, Bacillusselenitireducens, Exiguobacterium sibiricum, Lactobacillus delbrueckii,Lactobacillus salivarius, Microscilla marina, Burkholderiales bacterium,Polaromonas naphthalenivorans, Polaromonas sp., Crocosphaera watsonii,Cyanothece sp., Microcystis aeruginosa, Synechococcus sp., Acetohalobiumarabaticum, Ammonifex degensii, Caldicelulosiruptor becscii, CandidatusDesulforudis, Clostridium botulinum, Clostridium difficile, Finegoldiamagna, Natranaerobius thermophilus, Pelotomaculumthermopropionicum,Acidithiobacillus caldus, Acidithiobacillus ferrooxidans, Allochromatiumvinosum, Marinobacter sp., Nitrosococcus halophilus, Nitrosococcuswatsoni, Pseudoalteromonas haloplanktis, Ktedonobacter racemifer,Methanohalobium evestigatum, Anabaena variabilis, Nodularia spumigena,Nostoc sp., Arthrospira maxima, Arthrospira platensis, Arthrospira sp.,Lyngbya sp., Microcoleus chthonoplastes, Oscillatoria sp., Petrotogamobilis, Thermosipho africanus, Acaryochloris marina, or any specieswhich encodes a CRISPR nuclease with a known PAM sequence. CRISPRnucleases encoded by uncultured bacteria may also be used in the contextof the invention. (See Burstein et al. Nature, 2017). Variants of CRIPSRproteins having known PAM sequences e.g., SpCas9 D1135E variant, SpCas9VQR variant, SpCas9 EQR variant, or SpCas9 VRER variant may also be usedin the context of the invention.

Thus, an RNA guided DNA nuclease of a CRISPR system, such as a Cas9protein or modified Cas9 or homolog or ortholog of Cas9, or other RNAguided DNA nucleases belonging to other types of CRISPR systems, such asCpfl and its homologs and orthologs, may be used in the compositions ofthe present invention. Additional CRISPR nucleases may also be used, forexample, the nucleases described in PCT International ApplicationPublication Nos. WO2020/223514 and WO2020/223553, which are herebyincorporated by reference.

In certain embodiments, the CRIPSR nuclease may be a “functionalderivative” of a naturally occurring Cas protein. A “functionalderivative” of a native sequence polypeptide is a compound having aqualitative biological property in common with a native sequencepolypeptide. “Functional derivatives” include, but are not limited to,fragments of a native sequence and derivatives of a native sequencepolypeptide and its fragments, provided that they have a biologicalactivity in common with a corresponding native sequence polypeptide. Abiological activity contemplated herein is the ability of the functionalderivative to hydrolyze a DNA substrate into fragments. The term“derivative” encompasses both amino acid sequence variants ofpolypeptide, covalent modifications, and fusions thereof. Suitablederivatives of a Cas polypeptide or a fragment thereof include but arenot limited to mutants, fusions, covalent modifications of Cas proteinor a fragment thereof. Cas protein, which includes Cas protein or afragment thereof, as well as derivatives of Cas protein or a fragmentthereof, may be obtainable from a cell or synthesized chemically or by acombination of these two procedures. The cell may be a cell thatnaturally produces Cas protein, or a cell that naturally produces Casprotein and is genetically engineered to produce the endogenous Casprotein at a higher expression level or to produce a Cas protein from anexogenously introduced nucleic acid, which nucleic acid encodes a Casthat is same or different from the endogenous Cas. In some cases, thecell does not naturally produce Cas protein and is geneticallyengineered to produce a Cas protein.

In some embodiments, the CRISPR nuclease is Cpfl. Cpfl is a singleRNA-guided endonuclease which utilizes a T-rich protospacer-adjacentmotif. Cpfl cleaves DNA via a staggered DNA double-stranded break. TwoCpfl enzymes from Acidaminococcus and Lachnospiraceae have been shown tocarry out efficient genome-editing activity in human cells. (See Zetscheet al., 2015).

Thus, an RNA guided DNA nuclease of a Type II CRISPR System, such as aCas9 protein or modified Cas9 or homologs, orthologues, or variants ofCas9, or other RNA guided DNA nucleases belonging to other types ofCRISPR systems, such as Cpfl and its homologs, orthologues, or variants,may be used in the present invention.

In some embodiments, the guide molecule comprises one or more chemicalmodifications which imparts a new or improved property (e.g., improvedstability from degradation, improved hybridization energetics, orimproved binding properties with an RNA guided DNA nuclease). Suitablechemical modifications include, but are not limited to: modified bases,modified sugar moieties, or modified inter-nucleoside linkages.Non-limiting examples of suitable chemical modifications include:4-acetylcytidine, 5-(carboxyhydroxymethyl)uridine, 2′-O-methylcytidine,5-carboxymethylaminomethyl-2-thiouridine,5-carboxymethylammomethyluridine, dihydrouridine,2′-O-methylpseudouridine, “beta, D-galactosylqueuosine”,2′-O-methylguanosine, inosine, N6-isopentenyladenosine,1-methyladenosine, 1-methylpseudouridine, 1-methylguanosine,1-methylinosine, “2,2-dimethylguanosine”, 2-methyladenosine,2-methylguanosine, 3-methylcytidine, 5-methylcytidine,N6-methyladenosine, 7-methylguanosine, 5-methylaminomethylundine,5-methoxyaminomethyl-2-thiouridine, “beta, D-mannosylqueuosine”,5-methoxycarbonylmethyl-2-thiouridine, 5-methoxycarbonylmethyluridine,5-methoxyuridine, 2-methylthio-N6-isopentenyladenosine,N-((9-beta-D-ribofuranosyl-2-methylthiopurine-6-yl)carbamoyl)threonine,N-((9-beta-D-ribofuranosylpurine-6-yl)N-methylcarbamoyl)threonine,uridine-5-oxyacetic acid-methylester, uridine-5-oxyacetic acid,wybutoxosine, queuosine, 2-thiocytidine, 5-methyl-2-thiouridine,2-thiouridine, 4-thiouridine, 5-methyluridine,N-((9-beta-D-ribofmanosylpurine-6-yl)-carbamoyl)threonine,2′-O-methyl-5-methyluridine, 2′-O-methyluridine, wybutosine,“3-(3-amino-3-carboxy-propyl)uridine, (acp3)u”, 2′-0-methyl (M),3′-phosphorothioate (MS), 3′-thioPACE (MSP), pseudouridine, or 1-methylpseudo-uridine. Each possibility represents a separate embodiment of thepresent invention.

Guide Sequences Which Specifically Target a Mutant Allele

A given gene may contain thousands of SNPs. Utilizing a 25 base pairtarget window for targeting each SNP in a gene would require hundreds ofthousands of guide sequences. Any given guide sequence when utilized totarget a SNP may result in degradation of the guide sequence, limitedactivity, no activity, or off-target effects. Accordingly, suitableguide sequences are necessary for targeting a given gene. By the presentinvention, a novel set of guide sequences have been identified forknocking out expression of a mutated SAMD9 protein, inactivating amutant SAMD9 gene allele, and treating MIRAGE syndrome.

The present disclosure provides guide sequences capable of specificallytargeting a mutated allele for inactivation while leaving the functionalallele unmodified. The guide sequences of the present invention aredesigned to, and are most likely to, specifically differentiate betweena mutated allele and a functional allele. Of all possible guidesequences which target a mutated allele desired to be inactivated, thespecific guide sequences disclosed herein are specifically effective tofunction with the disclosed embodiments.

Briefly, the guide sequences may have properties as follows: (1) targetSNP/insertion/deletion/indel with a high prevalence in the generalpopulation, in a specific ethnic population or in a patient populationis above 1% and the SNP/insertion/deletion/indel heterozygosity rate inthe same population is above 1%; (2) target a location of aSNP/insertion/deletion/indel proximal to a portion of the gene e.g.,within 5k bases of any portion of the gene, for example, a promoter, aUTR, an exon or an intron; and (3) target a mutant allele using an RNAmolecule which targets a founder or common pathogenic mutations for thedisease/gene. In some embodiments, the prevalence of theSNP/insertion/deletion/indel in the general population, in a specificethnic population or in a patient population is above 1%, 2%, 3%, 4%,5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, or 15% and theSNP/insertion/deletion/indel heterozygosity rate in the same populationis above 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, or15%. Each possibility represents a separate embodiment and may becombined at will.

For each gene, according to SNP/insertion/deletion/indel any one of thefollowing strategies may be used to deactivate the mutated allele: (1)Knockout strategy using one RNA molecule - one RNA molecule is utilizedto direct a CRISPR nuclease to a mutated allele and create adouble-strand break (DSB) leading to formation of a frameshift mutationin an exon or in a splice site region of the mutated allele, oralternatively one RNA molecule is utilized to target an intron of amutated allele leading to introduction of a synthetic splice donor byHDR; (2) Excision of the coding exon using two RNA molecules, forexample, a first RNA molecule targets a SNP position of an exon of themutated allele and a second, non-discriminatory RNA molecule targets asequence within flanking the exon; (3) Excision of the polyadenylationsignal using two RNA molecules, for example, a first RNA moleculetargets a SNP position in the 3′UTR and a second, non-discriminatory RNAmolecule targets a sequences downstream of the polyadenylation signal.Alternatively, the first RNA molecule targets a SNP position locateddownstream of the polyadenylation signal and the second,non-discriminatory RNA molecule targets a sequence upstream of thepolyadenylation signal.

Based on the locations of identified SNPs/insertions/deletions/indelsfor each mutant allele, any one of, or a combination of, theabove-mentioned methods to deactivate the mutant allele may be utilized.

In some embodiments of the present invention, one RNA molecule is usedto target a SNP, and the location of the SNP is in an exon or in closeproximity (e.g., within 20 base pairs) to a splice site between anintron and an exon. In some embodiments, two RNA molecules are used andmay target two SNPs, such that the first SNP is upstream of the firstexon e.g., within the 5′ untranslated region, within the promoter, orwithin the first two kilobases 5′ of the transcription start site, andthe second SNP is downstream of the first SNP e.g., within the first twokilobases 5′ of the transcription start site, within an intron, orwithin an exon.

Guide sequences of the present invention may target a SNP in theupstream portion of the targeted gene, preferably upstream of the lastexon of the targeted gene. Guide sequences may target a SNP upstream tothe first exon, for example within the 5′ untranslated region, withinthe promoter, or within the first 4-5 kilobases 5′ of the transcriptionstart site.

Guide sequences of the present invention may also target a SNP withinclose proximity (e.g., within 50 base pairs, more preferably with 20base pairs) to a known protospacer adjacent motif (PAM) site.

Guide sequences of the present invention may: (1) target a heterozygousSNP for the targeted gene; (2) target a heterozygous SNP upstream ordownstream of the gene; (3) target a SNP with a prevalence of theSNP/insertion/deletion/indel in the general population, in a specificethnic population, or in a patient population above 1%; (4) have aguanine-cytosine content of greater than 30% and less than 85%; (5) haveno repeat of four or more thymine/uracil or eight or more guanine,cytosine, or adenine; and (6) have low or no off-targeting identified byoff-target analysis. Guide sequences of the present invention maysatisfy any one of the above criteria and are most likely todifferentiate between a mutated allele from its corresponding functionalallele.

In some embodiments of the present invention, a SNP targeted by an RNAmolecule may be upstream or downstream of the gene. In some embodimentsof the present invention, the SNP is within 4,000 base pairs of thegene.

in some embodiments of the present invention, at least one nucleotidewhich differs between the mutated allele and the functional allele isupstream, downstream or within the sequence of the disease-causingmutation of the gene of interest. The at least one nucleotide whichdiffers between the mutated allele and the functional allele may bewithin an exon or within an intron of the gene of interest. In someembodiments, the at least one nucleotide which differs between themutated allele and the functional allele is within an exon of the geneof interest. In some embodiments, the at least one nucleotide whichdiffers between the mutated allele and the functional allele is withinan intron or the exon of the gene of interest, in close proximity to thesplice site between the intron and the exon e.g., 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29 or 30 nucleotides upstream or downstream to the splicesite. Each possibility represents a separate embodiment.

In some embodiments, the at least one nucleotide is a single nucleotidepolymorphism (SNP). In some embodiments, each of the nucleotide variantsof the SNP may be expressed in the mutated allele. In some embodiments,the SNP may be a founder or common pathogenic mutation.

Guide sequences may target a SNP which has both (1) a high prevalence inthe general population e.g., above 1% in the population; and (2) a highheterozygosity rate in the population, e.g., above 1%. Guide sequencesmay target a SNP that is globally distributed. A SNP may be a founder orcommon pathogenic mutation. In some embodiments, the prevalence in thegeneral population is above 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%,11%, 12%, 13%, 14%, or 15%. Each possibility represents a separateembodiment. In some embodiments, the heterozygosity rate in thepopulation is above 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%,13%, 14%, or 15%. Each possibility represents a separate embodiment.

In some embodiments, the at least one nucleotide which differs betweenthe mutated allele and the functional allele is linked to/co-exists withthe disease-causing mutation in high prevalence in a population. In suchembodiments, “high prevalence” refers to at least 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100%. Each possibility represents a separateembodiment of the present invention. In one embodiment, the at least onenucleotide which differs between the mutated allele and the functionalallele, is a disease-associated mutation. In some embodiments, the SNPis highly prevalent in the population. In such embodiments, “highlyprevalent” refers to at least 10%, 11%, 12%, 13%, 14%, 15%, 20%, 30%,40%, 50%, 60%, or 70% of a population. Each possibility represents aseparate embodiment of the present invention.

Delivery to Cells

The RNA molecule compositions described herein may be delivered to atarget cell by any suitable means. RNA molecule compositions of thepresent invention may be targeted to any cell which contains and/orexpresses a mutated allele, including any mammalian or plant cell. Forexample, in one embodiment the RNA molecule specifically targets amutated SAMD9 allele and the target cell is an HSC. The delivery to thecell may be performed in-vitro, ex-vivo, or in-vivo. Further, thenucleic acid compositions described herein may be delivered as one ormore of DNA molecules, RNA molecules, Ribonucleoproteins (RNP), nucleicacid vectors, or any combination thereof.

In some embodiments, the RNA molecule comprises a chemical modification.Non-limiting examples of suitable chemical modifications include2′-0-methyl (M), 2′-0-methyl, 3′phosphorothioate (MS) or 2′-0-methyl, 3‘thioPACE (MSP), pseudouridine, and 1-methyl pseudouridine. Eachpossibility represents a separate embodiment of the present invention.

Any suitable viral vector system may be used to deliver nucleic acidcompositions e.g., the RNA molecule compositions of the subjectinvention. Conventional viral and non-viral based gene transfer methodscan be used to introduce nucleic acids and target tissues. In certainembodiments, nucleic acids are administered for in vivo or ex vivo genetherapy uses. Non-viral vector delivery systems include naked nucleicacid, and nucleic acid complexed with a delivery vehicle such as aliposome or poloxamer. For a review of gene therapy procedures, seeAnderson (1992); Nabel & Felgner (1993); Mitani & Caskey (1993); Dillon(1993); Miller (1992); Van Brunt (1988); Vigne (1995); Kremer &Perricaudet (1995); Haddada et al. (1995); and Yu et al. (1994).

Methods of non-viral delivery of nucleic acids and/or proteins includeelectroporation, lipofection, microinjection, biolistics, particle gunacceleration, virosomes, liposomes, immunoliposomes, lipid nanoparticles(LNPs), polycation or lipid:nucleic acid conjugates, artificial virions,and agent-enhanced uptake of nucleic acids or can be delivered to plantcells by bacteria or viruses (e.g., Agrobacterium, Rhizobium sp. NGR234,Sinorhizoboiummeliloti, Mesorhizobium loti, tobacco mosaic virus, potatovirus X, cauliflower mosaic virus and cassava vein mosaic virus). (See,e.g., Chung et al., 2006). Sonoporation using, e.g., the Sonitron 2000system (Rich-Mar), can also be used for delivery of nucleic acids.Cationic-lipid mediated delivery of proteins and/or nucleic acids isalso contemplated as an in vivo, ex vivo, or in vitro delivery method.(See Zuris et al. (2015); see also Coelho et al. (2013); Judge et al.(2006); and Basha et al. (2011)).

Non-viral vectors, such as transposon-based systems e.g. recombinantSleeping Beauty transposon systems or recombinant PiggyBac transposonsystems, may also be delivered to a target cell and utilized fortransposition of a polynucleotide sequence of a molecule of thecomposition or a polynucleotide sequence encoding a molecule of thecomposition in the target cell.

Additional exemplary nucleic acid delivery systems include thoseprovided by Amaxa.RTM. Biosystems (Cologne, Germany), Maxcyte, Inc.(Rockville, Md.), BTX Molecular Delivery Systems (Holliston, Mass.) andCopernicus Therapeutics Inc., (see, e.g., U.S. Pat. No. 6,008,336).Lipofection is described in e.g., U.S. Pat. No. 5,049,386, U.S. Pat. No.4,946,787; and U.S. Pat. No. 4,897,355, and lipofection reagents aresold commercially (e.g., Transfectam.TM., Lipofectin.TM. andLipofectamine.TM. RNAiMAX). Cationic and neutral lipids that aresuitable for efficient receptor-recognition lipofection ofpolynucleotides include those disclosed in PCT International PublicationNos. WO/1991/017424 and WO/1991/016024. Delivery can be to cells (exvivo administration) or target tissues (in vivo administration).

The preparation of lipid:nucleic acid complexes, including targetedliposomes such as immunolipid complexes, is well known to one of skillin the art (see, e.g., Crystal, Science (1995); Blaese et al., (1995);Behr et al., (1994); Remy et al. (1994); Gao and Huang (1995); Ahmad andAllen (1992); U.S. Pat. Nos. 4,186,183; 4,217,344; 4,235,871; 4,261,975;4,485,054; 4,501,728; 4,774,085; 4,837,028; and 4,946,787).

Additional methods of delivery include the use of packaging the nucleicacids to be delivered into EnGeneIC delivery vehicles (EDVs). These EDVsare specifically delivered to target tissues using bispecific antibodieswhere one arm of the antibody has specificity for the target tissue andthe other has specificity for the EDV. The antibody brings the EDVs tothe target cell surface and then the EDV is brought into the cell byendocytosis. Once in the cell, the contents are released (See MacDiarmidet al., 2009).

The use of RNA or DNA viral based systems for viral mediated delivery ofnucleic acids take advantage of highly evolved processes for targeting avirus to specific cells in the body and trafficking the viral payload tothe nucleus. Viral vectors can be administered directly to patients (invivo) or they can be used to treat cells in vitro and the modified cellsare administered to patients (ex vivo). Conventional viral based systemsfor the delivery of nucleic acids include, but are not limited to,retroviral, lentivirus, adenoviral, adeno-associated, vaccinia andherpes simplex virus vectors for gene transfer.

The tropism of a retrovirus can be altered by incorporating foreignenvelope proteins, expanding the potential target population of targetcells. Lentiviral vectors are retroviral vectors that are able totransduce or infect non-dividing cells and typically produce high viraltiters. Selection of a retroviral gene transfer system depends on thetarget tissue. Retroviral vectors are comprised of cis-acting longterminal repeats with packaging capacity for up to 6-10 kb of foreignsequence. The minimum cis-acting LTRs are sufficient for replication andpackaging of the vectors, which are then used to integrate thetherapeutic gene into the target cell to provide permanent transgeneexpression. Widely used retroviral vectors include those based uponmurine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), SimianImmunodeficiency virus (SIV), human immunodeficiency virus (HIV), andcombinations thereof (See, e.g., Buchschacher et al. (1992); Johann etal. (1992); Sommerfelt et al. (1990); Wilson et al. (1989); Miller etal. (1991); PCT International Publication No. WO/1994/026877A1).

At least six viral vector approaches are currently available for genetransfer in clinical trials, which utilize approaches that involvecomplementation of defective vectors by genes inserted into helper celllines to generate the transducing agent.

pLASN and MFG-S are examples of retroviral vectors that have been usedin clinical trials (See Dunbar et al., 1995; Kohn et al., 1995; Malechet al., 1997). PA317/pLASN was the first therapeutic vector used in agene therapy trial (Blaese et al., 1995). Transduction efficiencies of50% or greater have been observed for MFG-S packaged vectors. (Ellem etal., (1997); Dranoff et al., 1997).

Packaging cells are used to form virus particles that are capable ofinfecting a host cell. Such cells include 293 cells, which packageadenovirus, AAV, and Psi-2 cells or PA317 cells, which packageretrovirus. Viral vectors used in gene therapy are usually generated bya producer cell line that packages a nucleic acid vector into a viralparticle. The vectors typically contain the minimal viral sequencesrequired for packaging and subsequent integration into a host (ifapplicable), other viral sequences being replaced by an expressioncassette encoding the protein to be expressed. The missing viralfunctions are supplied in trans by the packaging cell line. For example,AAV vectors used in gene therapy typically only possess invertedterminal repeat (ITR) sequences from the AAV genome which are requiredfor packaging and integration into the host genome. Viral DNA ispackaged in a cell line, which contains a helper plasmid encoding theother AAV genes, namely rep and cap, but lacking ITR sequences. The cellline is also infected with adenovirus as a helper. The helper viruspromotes replication of the AAV vector and expression of AAV genes fromthe helper plasmid. The helper plasmid is not packaged in significantamounts due to a lack of ITR sequences. Contamination with adenoviruscan be reduced by, e.g., heat treatment to which adenovirus is moresensitive than AAV. Additionally, AAV can be produced at clinical scaleusing baculovirus systems (see U.S. Pat. No. 7,479,554).

In many gene therapy applications, it is desirable that the gene therapyvector be delivered with a high degree of specificity to a particulartissue type. Accordingly, a viral vector can be modified to havespecificity for a given cell type by expressing a ligand as a fusionprotein with a viral coat protein on the outer surface of the virus. Theligand is chosen to have affinity for a receptor known to be present onthe cell type of interest. For example, Han et al. (1995) reported thatMoloney murine leukemia virus can be modified to express human heregulinfused to gp70, and the recombinant virus infects certain human breastcancer cells expressing human epidermal growth factor receptor. Thisprinciple can be extended to other virus-target cell pairs, in which thetarget cell expresses a receptor and the virus expresses a fusionprotein comprising a ligand for the cell-surface receptor. For example,filamentous phage can be engineered to display antibody fragments (e.g.,FAB or Fv) having specific binding affinity for virtually any chosencellular receptor. Although the above description applies primarily toviral vectors, the same principles can be applied to nonviral vectors.Such vectors can be engineered to contain specific uptake sequenceswhich favor uptake by specific target cells.

Gene therapy vectors can be delivered in vivo by administration to anindividual patient, typically by systemic administration (e.g.,intravitreal, intravenous, intraperitoneal, intramuscular, subdermal, orintracranial infusion) or topical application, as described below.Alternatively, vectors can be delivered to cells ex vivo, such as cellsexplanted from an individual patient (e.g., lymphocytes, bone marrowaspirates, tissue biopsy) or universal donor hematopoietic stem cells,followed by reimplantation of the cells into a patient, optionally afterselection for cells which have incorporated the vector. A non-limitingexemplary ex vivo approach may involve removal of tissue (e.g.,peripheral blood, bone marrow, and spleen) from a patient for culture,nucleic acid transfer to the cultured cells (e.g., hematopoietic stemcells), followed by grafting the cells to a target tissue (e.g., bonemarrow, and spleen) of the patient. In some embodiments, the stem cellor hematopoietic stem cell may be further treated with a viabilityenhancer.

Ex vivo cell transfection for diagnostics, research, or for gene therapy(e.g., via re-infusion of the transfected cells into the host organism)is well known to those of skill in the art. In a preferred embodiment,cells are isolated from the subject organism, transfected with a nucleicacid composition, and re-infused back into the subject organism (e.g.,patient). Various cell types suitable for ex vivo transfection are wellknown to those of skill in the art (See, e.g., Freshney, “Culture ofAnimal Cells, A Manual of Basic Technique and Specialized Applications(6th edition, 2010) and the references cited therein for a discussion ofhow to isolate and culture cells from patients).

Suitable cells include, but are not limited to, eukaryotic cells and/orcell lines. Non-limiting examples of such cells or cell lines generatedfrom such cells include COS, CHO (e.g., CHO--S, CHO-K1, CHO-DG44,CHO-DUXB11, CHO-DUKX, CHOK1SV), VERO, MDCK, WI38, V79, B14AF28-G3, BHK,HaK, NSO, SP2/0-Ag14, HeLa, HEK293 (e.g., HEK293-F, HEK293-H, HEK293-T),perC6 cells, any plant cell (differentiated or undifferentiated), aswell as insect cells such as Spodopterafugiperda (Sf), or fungal cellssuch as Saccharomyces, Pichia and Schizosaccharomyces. In certainembodiments, the cell line is a CHO-K1, MDCK or HEK293 cell line.Additionally, primary cells may be isolated and used ex vivo forreintroduction into the subject to be treated following treatment with aguided nuclease system (e.g. CRISPR/Cas). Suitable primary cells includeperipheral blood mononuclear cells (PBMC), and other blood cell subsetssuch as, but not limited to, CD4+ T cells or CD8+ T cells. Suitablecells also include stem cells such as, by way of example, embryonic stemcells, induced pluripotent stem cells, hematopoietic stem cells (CD34+),neuronal stem cells and mesenchymal stem cells.

In one embodiment, stem cells are used in ex vivo procedures for celltransfection and gene therapy. The advantage to using stem cells is thatthey can be differentiated into other cell types in vitro, or can beintroduced into a mammal (such as the donor of the cells) where theywill engraft in the bone marrow. Methods for differentiating CD34+ cellsin vitro into clinically important immune cell types using cytokinessuch a GM-CSF, IFN-gamma, and TNF-alpha are known (as a non-limitingexample see, Inaba et al., 1992).

Stem cells are isolated for transduction and differentiation using knownmethods. For example, stem cells are isolated from bone marrow cells bypanning the bone marrow cells with antibodies which bind unwanted cells,such as CD4+ and CD8+ (T cells), CD45+(panB cells), GR-1 (granulocytes),and Iad (differentiated antigen presenting cells) (as a non-limitingexample, see Inaba et al., 1992). Stem cells that have been modified mayalso be used in some embodiments.

Vectors (e.g., retroviruses, liposomes, etc.) containing therapeuticnucleic acid compositions can also be administered directly to anorganism for transduction of cells in vivo. Administration is by any ofthe routes normally used for introducing a molecule into ultimatecontact with blood or tissue cells including, but not limited to,injection, infusion, topical application (e.g., eye drops and cream) andelectroporation. Suitable methods of administering such nucleic acidsare available and well known to those of skill in the art, and, althoughmore than one route can be used to administer a particular composition,a particular route can often provide a more immediate and more effectivereaction than another route. According to some embodiments, thecomposition is delivered via IV injection.

Vectors suitable for introduction of transgenes into immune cells (e.g.,T-cells) include non-integrating lentivirus vectors. See, e.g., U.S.Pat. Publication No. 2009/0117617.

Pharmaceutically acceptable carriers are determined in part by theparticular composition being administered, as well as by the particularmethod used to administer the composition. Accordingly, there is a widevariety of suitable formulations of pharmaceutical compositionsavailable, as described below (See, e.g., Remington’s PharmaceuticalSciences, 17th ed., 1989).

In accordance with some embodiments, there is provided an RNA moleculewhich binds to/ associates with and/or directs the RNA guided DNAnuclease to a sequence comprising at least one nucleotide which differsbetween a mutated allele and a functional allele (e.g., SNP) of a geneof interest (i.e., a sequence of the mutated allele which is not presentin the functional allele). The sequence may be within the diseaseassociated mutation. The sequence may be upstream or downstream to thedisease associated mutation. Any sequence difference between the mutatedallele and the functional allele may be targeted by an RNA molecule ofthe present invention to inactivate the mutant allele, or otherwisedisable its dominant disease-causing effects, while preserving theactivity of the functional allele.

The disclosed compositions and methods may also be used in themanufacture of a medicament for treating dominant genetic disorders in apatient.

Mechanisms of Action for SAMD9 Knockout Methods

Without being bound by any theory or mechanism, the instant inventionmay be utilized to apply a CRISPR nuclease to process a mutatedpathogenic SAMD9 allele and not a functional SAMD9 allele, such as toprevent expression of the mutated pathogenic allele or to produce atruncated non-pathogenic peptide from the mutated pathogenic allele, inorder to prevent MIRAGE syndrome. A specific guide sequence may beselected from Table 1 based on the targeted SNP and the type of CRISPRnuclease used (required PAM sequence).

The SAMD9 gene is located in chromosome 7 and encodes the SAMD9 protein.One optional strategy to knockout a mutated SAMD9 allele is to truncateit by targeting a SNP position in a coding exon of SAMD9 using one RNAmolecule. Truncation may also be achieved by excision of an exon usingtwo RNA molecules, wherein one of the RNA molecules targets an allelespecific sequence in a SNP position and the other RNA molecule is anon-discriminatory guide that targets a sequence flanking the codingexon. Another optional strategy to knockout SAMD9 is by excision of itspolyadenylation signal using a first RNA molecule to target a SNPposition in the 3′UTR and a second, non-discriminatory RNA to targetdownstream of the polyadenylation signal. Alternatively, excision of theSAMD9 polyadenylation signal may be performed by using a first RNAmolecule to target a SNP position located downstream of thepolyadenylation signal and a second, non-discriminatory RNA molecule totarget a sequence upstream of the polyadenylation signal. Excision of aportion of a mutated SAMD9 allele may also be achieved by mediating aDSB in an intron flanking the desired exon and a region downstream ofthe desired exon. Yet another optional strategy is to introduce by HDR asynthetic splice acceptor site in Intron 2, such that the coding exon isno longer expressed.

Examples of RNA Guide Sequences Which Specifically Target MutatedAlleles of SAMD9 Gene

Disclosures which include sequences that may interact with a SARM1sequence in some form include PCT International Application PublicationNos. WO2020/191171, WO2013/081864, WO2017/072590, WO2019/081982,WO2018/154412, Japanese Application Publication No. 2008/504843, andU.S. Publication Nos. 2006/0019284 and 2006/0003322, each of which arehereby incorporated by reference. Although a large number of guidesequences can be designed to target a mutated allele, the nucleotidesequences described in Tables 2 identified by SEQ ID NOs: 1-20640 belowwere specifically selected to effectively implement the methods setforth herein and to effectively discriminate between alleles.

Table 1 shows guide sequences designed for use as described in theembodiments above to associate with different SNPs or pathogenicmutations within a sequence of a mutated SAMD9 allele. Each engineeredguide molecule is further designed such as to associate with a targetgenomic DNA sequence of interest that lies next to a protospaceradjacent motif (PAM), e.g., a PAM matching the sequence NGG or NAG,where “N” is any nucleobase. The guide sequences were designed to workin conjunction with one or more different CRISPR nucleases, including,but not limited to, e.g. SpCas9WT (PAM SEQ: NGG), SpCas9.VQR.1 (PAM SEQ:NGAN), SpCas9.VQR.2 (PAM SEQ: NGNG), SpCas9.EQR (PAM SEQ: NGAG),SpCas9.VRER (PAM SEQ: NGCG), SaCas9WT (PAM SEQ: NNGRRT), SpRY (PAM SEQ:NRN or NYN), NmCas9WT (PAM SEQ: NNNNGATT), Cpfl (PAM SEQ: TTTV), orJeCas9WT (PAM SEQ: NNNVRYM). RNA molecules of the present invention areeach designed to form complexes in conjunction with one or moredifferent CRISPR nucleases and designed to target polynucleotidesequences of interest utilizing one or more different PAM sequencesrespective to the CRISPR nuclease utilized.

TABLE 1 Guide sequence portions designed to associate with specificSAMD9 gene targets Target SEQ ID NOs: of 20-nucleotide guide sequenceportions SEQ ID NOs: of 21-nucleotide guide sequence portions SEQ IDNOs: of 22-nucleotide guide sequence portions 7:93101391_C_G 1-52 53-106107-162 7:93101435_G_A 163-214 215-268 269-324 7:93101512_C_T 325-376377-430 431-486 7:93101540_C_A 487-538 539-592 593-648 7:93101615_T_C649-700 701-754 755-810 7:93101761_AGTT_A 811-852 853-896 897-9427:93101900_G_A 943-994 995-1048 1049-1104 7:93102220_C_T 1105-11561157-1210 1211-1266 7:93102221_G_A 1106-1107, 1109, 1113-1114, 1120,1127, 1142, 1146, 1154, 1267-1308 1158, 1161, 1165, 1172, 1179, 1190,1194, 1198-1199, 1208, 1309-1352 1212, 1219, 1226, 1244, 1248,1252-1253, 1259, 1262-1263, 1353-1398 7:93102242_G_T 1399-1444 1445-14861487-1536 7:93102259_G_A 1537-1588 1589-1641 1642-1697 7:93102368_T_C1698-1749 1750-1803 1804-1859 7:93102514_G_A 1860-1911 1912-19631964-2019 7:93102593_G_A 2020-2071 2072-2125 2126-2181 7:93102692_C_G2182-2233 2234-2287 2288-2343 7:93102717_G_T 2344-2385 2386-24212422-2463 7:93103150_AT_GA 2464-2515 2516-2569 2570-2625 7:93103151_T_C2466, 2472, 2485-2486, 2496, 2499, 2503, 2508, 2513, 2515, 2626-26672518, 2524, 2532, 2539, 2543, 2553, 2557, 2562, 2567, 2569, 2668-27112572, 2576, 2579, 2581, 2587, 2594, 2598, 2613, 2623, 2625, 2712-27577:93103153_C_T 2485-2486, 2503, 2508, 2513, 2515, 2640, 2665, 2758-28012524, 2532, 2539, 2557, 2562, 2569, 2673, 2689, 2802-2847 2572, 2576,2579, 2587, 2594, 2625, 2736, 2752, 2848-2895 7:93103178_C_T 2896-29472948-3001 3002-3057 7:93103253_C_A 3058-3109 3110-3163 3164-32197:93103393_C_T 3220-3271 3272-3324 3325-3379 7:93103588_C_CT 3380-34273428-3477 3478-3529 7:93103598_T_A 3530-3581 3582-3635 3636-36917:93103628_G_A 3692-3743 3744-3787 3788-3835 7:93103679_C_T 3836-38873888-3937 3938-3991 7:93103765_G_A 3992-4043 4044-4097 4098-41537:93103772_G_T 4154-4205 4206-4259 4260-4315 7:93103793_C_T 4316-43674368-4421 4422-4477 7:93103851_G_T 4478-4529 4530-4583 4584-46397:93103900_A_G 4640-4691 4692-4745 4746-4801 7:93103916_T_C 4802-48534854-4907 4908-4963 7:93103933_G_T 4964-5015 5016-5069 5070-51257:93103938_GT_G 5126-5169 5170-5215 5216-5263 7:93104044_C_T 5264-53155316-5369 5370-5425 7:93104176_A_G 5426-5477 5478-5531 5532-55877:93104296_ATT_A 5588-5635 5636-5685 5686-5737 7:93104449_T_A 5738-57895790-5843 5844-5899 7:93104694_TAC_GCA 7:93104695_AC_GA 5900-5951 5900,5906, 5910, 5921, 5924, 5926-5927, 5932, 5939, 5941, 6062-6103 5952-60055958, 5962, 5973, 5976, 5978, 5980, 5985, 5992, 5994, 6001, 6104-61476006-6061 6012, 6014, 6029, 6032, 6034, 6036, 6041, 6048, 6057, 6060,6148-6193 7:93104722_C_T 6194-6245 6246-6299 6300-6355 7:93105043_A_G6356-6407 6408-6459 6460-6515 7:93105103_A_G 6516-6567 6568-66186619-6673 7:93105122_G_A 6674-6707 6708-6712 6713-6723 7:93105295_A_G6724-6775 6776-6829 6830-6885 7:93105436_C_T 6886-6937 6938-69916992-7047 7:93105485_T_G 7048-7099 7100-7153 7154-7209 7:93105638_G_A7210-7261 7262-7311 7312-7364 7:93105781_C_T 7365-7416 7417-74707471-7526 7:93105965_CT_C 7527-7571 7572-7617 7618-7663 7:93106002_GT_G7664-7713 7714-7765 7766-7819 7:93106003_T_A 7668, 7672, 7678,7691-7692, 7697-7699, 7703, 7705, 7708, 7712, 7820-7859 7718, 7722,7726, 7729, 7741, 7743-7744, 7749-7750, 7757, 7760, 7764, 7860-79017770, 7774, 7778-7779, 7782, 7794, 7796-7797, 7803, 7806, 7811, 7818,7902-7945 7:93106096_A_G 7946-7997 7998-8051 8052-8107 7:93096736_CT_Crs201891812_REF 8108-8127 8128-8143 8144-8159 7:93096736_CT_Crs201891812_SNP 8115, 8119, 8121, 8160 8134, 8137 8153, 8156, 81617:93096863_C_T rs73216083_REF 8162-8213 8214-8265 8266-83217:93096863_C_T rs73216083_SNP 8162-8164, 8166, 8168, 8171, 8178, 8180,8183, 8198, 8200, 8203, 8322-8361 8214-8217, 8220, 8223, 8231, 8234,8249-8250, 8362-8403 8266-8269, 8271, 8273, 8276, 8283-8284, 8303,8305-8306, 8404-8447 7:93096894_C_CTTTT rs542330750_REF 8448-84668467-8486 8487-8507 7:93097829_G_A rs7798225_REF 8508-8559 8560-86138614-8669 7:93097829_G_A rs7798225_SNP 8508, 8513, 8515, 8523,8527-8528, 8531, 8533, 8546, 8556, 8558-8559, 8670-8709 8560, 8567,8575, 8579-8581, 8584, 8586, 8599, 8603, 8612-8613, 8710-8751 8614,8621, 8629, 8633-8635, 8638, 8640, 8657-8658, 8665, 8669, 8752-87957:93099114_C_T rs10953089_REF 8796-8831 8832-8861 8862-88967:93099114_C_T rsl0953089_SNP 8805, 8808, 8811-8812, 8818, 8822-8823,8827-8831, 8897-8912 8841, 8844-8845, 8849, 8853-8854, 8858-8861,8913-8922 8869, 8872, 8875-8877, 8881, 8885-8886, 8892, 8895-8896,8923-8934 7:93099215_G_A rs10953090_REF 8935-8986 8987-9040 9041-90967:93099215_G_A rs10953090_SNP 8938, 8941, 8945-8946, 8953, 8959, 8962,8968-8969, 8973, 8975, 8981, 9097-9134 8990, 8993, 8997-8998, 9005,9014, 9020-9021, 9025-9026, 9034, 9037, 9135-9176 9044, 9047, 9051,9059, 9073, 9075-9076, 9080-9081, 9089, 9092-9093, 9177-92207:93099485_T_C rs10277338_REF 9221-9266 9267-9302 9303-93467:93099485_T_C rs10277338_SNP 9223, 9230, 9233, 9235, 9238, 9246, 9249,9254-9255, 9260, 9262, 9264, 9347-9386 9274, 9276-9277, 9280, 9285,9287, 9292-9293, 9297, 9299-9300, 9302, 9387-9426 9310, 9314, 9317,9319, 9323-9324, 9326, 9334-9335, 9341-9342, 9344, 9427-94707:93100095_T_C rs71562815_REF 9471-9494 9495-9518 9519-95427:93100095_T_C rs71562815_SNP 9474, 9476-9478, 9480-9482, 9486-9487,9489, 9491, 9494, 9543-9582 9498, 9500-9501, 9504-9505, 9509-9512,9514-9515, 9518, 9583-9624 9522, 9524, 9527-9529, 9532-9536, 9539, 9542,9625-9668 7:93100248_G_T rs12333976_REF 9669-9712 9713-9744 9745-97787:93100248_G_T rs12333976_SNP 9673-9674, 9679, 9685, 9694, 9700,9779-9800 9715, 9718, 9724, 9730, 9736, 9741, 9801-9818 9747, 9756,9762, 9768, 9773, 9777, 9819-9840 7:93100656_GT_G rs3839837_REF9841-9862 9863-9883 9884-9905 7:93100656_GT_G rs3839837_SNP 9850,9856-9857, 9860, 9862, 9906 9871, 9873, 9881, 9883, 9907 9889, 9892,9894-9895, 9905, 9908 7:93104453_C_A rs10279499_REF 5744, 5746, 5765,5772, 5776, 5780, 5786, 5789, 9909-9952 5791, 5796, 5798, 5815, 5818,5825, 5840, 5843, 9953-9998 5845, 5852, 5854, 5869, 5872, 5880, 5891,5899, 9999-10046 7:93104453_C_A rs10279499_SNP 5744, 5765, 5772, 5780,9911, 9926, 9929-9930, 9932, 9934, 9938, 9948, 10047-10086 5791, 5796,5815, 5818, 9955, 9970, 9974, 9977, 9981, 9991, 9993-9994, 10087-101285845, 5854, 5869, 5891, 10001, 10004, 10017, 10024, 10028, 10038, 10040,10046, 10129-10172 7:93104662_G_A rs78564070_REF 10173-10224 10225-1027810279-10334 7:93104662_G_A rs78564070_SNP 10175, 10178, 10184, 10188,10196, 10201, 10206, 10208, 10213-10214, 10217, 10222, 10335-1037410230, 10236, 10240, 10242, 10249, 10254, 10261, 10265, 10267-10268,10271, 10276, 10375-10416 10284, 10290, 10296, 10303, 10308, 10315,10319, 10321-10322, 10327, 10331-10332, 10417-10460 7:93105138_A_Grs6965201_REF 6678-6679, 6681, 6688, 6692, 6696, 10461-10506 6710,10507-10547 6714, 6722, 10548-10592 7:93105138_A_G rs6965201_SNP10466-10467, 10473, 10477, 10485-10486, 10488, 10490-10491, 10497,10500, 10506, 10593-10632 10511-10512, 10518, 10520, 10523,10531-10533,10535, 10543, 10633-10674 10552-10554, 10561, 10573-10575, 10577, 10579,10586, 10588, 10675-10718 7:93105670_A_G rs6969691 REF 10719-1076110762-10801 10802-10844 7:93105670_A_G rs6969691_SNP 10721, 10726,10735, 10742-10743, 10746, 10752, 10845-10884 10764, 10768, 10776,10786, 10791, 10797, 10885-10922 10804, 10816, 10818, 10826, 10829,10834, 10840, 10923-10964 7:93106641_A_G rs2374627 REF 10965-1101611017-11069 11070-11125 7:93106641_A_G rs2374627_SNP 10971, 10978,10981-10982, 10996-10997, 10999, 11001, 11005-11007, 11011, 11126-1116511023, 11030, 11032, 11034-11035, 11049-11050, 11054, 11058, 11060,11064, 11166-11207 11073, 11077, 11084,11086, 11088-11089, 11096,11104-11105, 11109, 11115-11116, 11208-11251 7:93106866_A_Crs12668221_REF 11252-11303 11304-11357 11358-11413 7:93106866_A_Crs12668221_SNP 11259, 11269, 11272, 11275, 11277, 11279, 11288,11291-11292, 11298-11299, 11303, 11414-11453 11311, 11323, 11325, 11328,11332, 11341, 11344-11345, 11351-11352, 11356-11357, 11454-11495 11365,11372, 11379, 11381, 11384, 11388, 11400-11401, 11407-11408,11412-11413, 11496-11539 7:93107482_A_C rs28673511 REF 11540-1156711568-11591 11592-11620 7:93107482_A_C rs28673511_SNP 11540-11541,11544, 11547, 11553-11554, 11557, 11561, 11621-11648 11568-11570, 11572,11574, 11577, 11579, 11582,11649-11670 11592-11596, 11598, 11605, 11607,11610, 11671-11694 7:93107663_T_C rs10229795_REF 11695-11745 11746-1178711788-11833 7:93107663_T_C rs10229795_SNP 11699, 11708, 11713, 11718,11721, 11724, 11726, 11729, 11737-11738, 11744, 11834-11873 11753,11761, 11763, 11765, 11769, 11772, 11778, 11780, 11874-11915 11796,11804, 11806, 11808, 11811, 11813, 11822-11823, 11825, 11829,11916-11959 7:93107775_C_T rs7785869_REF 11960-12003 12004-1204712048-12091 7:93107775_C_T rs7785869_SNP 11969, 11977, 11979, 11988,11992, 11995, 12092-12129 12020, 12022, 12031, 12035, 12038, 12042,12130-12167 12063, 12065, 12068, 12079, 12082, 12086, 12168-122057:93108136_C_T rs67885698_REF 12206-12257 12258-12311 12312-123677:93108136_C_T rs67885698_SNP 12206-12208, 12211, 12218-12219, 12226,12233, 12238, 12245, 12252, 12255, 12368-12407 12258-12260, 12263,12270, 12272, 12277, 12280, 12292, 12299, 12306, 12309, 12408-1244912312-12314, 12324, 12326, 12331, 12345, 12347, 12354, 12361-12362,12365, 12450-12493 7:93108745_C_G rs6957832 REF 12494-12543 12544-1259712598-12653 7:93108925_C_T rs12704664_REF 12654-12665 12666-1267912680-12695 7:93108925_C_T rs12704664_SNP 12659-12662, 12664-12665,12696-12707 12672-12674, 12676, 12678-12679, 12708-12727 12683,12689-12690, 12692, 12694-12695, 12728-12755 7:93100828-7:93101327 (3′UTR downstream to the stop codon) 12756-13657 13658-14559 14560-154617:93099521-7:93100020 (3′ UTR upstream to the polyadenylation signal)15462-16255 16256-17073 17074-17909 7:93099413-7:93099913 (Intergenic)9221-9230, 9232-9264, 15463, 15465-15466, 15469, 15471, 15473-15478,15480-15482, 15484-15486, 15488-15491, 15494-15500, 15502-15503,15505-15508, 15512-15514, 15516-15521, 15523-15527, 15529-15530,15532-15537, 15539, 15545-15546, 15548-15556, 15558-15561, 15563-15565,15567-15574, 15576-15577, 15580- 9267-9302, 16257-16258, 16260-16261,16264, 16266, 16268-16273, 16275-16278, 16280-16282, 16284-16288,16292-16298, 16300-16301, 16303-16306, 16310-16312, 16314-16319,16321-16325, 16327-16328, 16330-16336, 16338, 16344-16345, 16347-16355,16357-16360, 16362-16364, 16366-16373, 16375-16376, 16379-16381,9303-9346, 17075-17076, 17078-17079, 17082, 17084, 17087-17092,17094-17097, 17099-17101, 17103-17108, 17112-17118, 17120-17121,17123-17126, 17130-17132, 17134-17139, 17141-17145, 17147-17148,17150-17156, 17158, 17164-17165, 17167-17176, 17178-17181, 17183-17185,17187-17194, 17196-17197, 17200-17202, 15582, 15584-15586, 15588,15591-15592, 15594-15601, 15603-15609, 15611-15615, 15617-15618,15620-15631, 15635-15637, 15639-15641, 15643-15646, 15648-15656,15658-15659, 15661-15663, 15672-15674, 15677, 15679, 15681-15682,15684-15689, 15691-15693, 15695-15697, 15699-15701, 15703-15704, 15707,15709-15711, 15713-15714, 15717-15723, 15725-15726, 15728-15731,15734-15738, 15741-15742, 15744-15746, 15748-15753, 15755, 15757-15763,15765-15766, 15768-15769, 15771, 15773-15781, 15784-15794, 15796-15798,15800-15804, 15807-15811, 15813, 15817-15822, 15824-15825, 15827-15831,15833-15837, 15840-15842, 15844-15849, 15851-15857, 15859-15865, 15867,15869, 15871-15874, 15876-15880, 16383-16385, 16387, 16390-16391,16393-16400, 16402-16408, 16410-16414, 16416-16417, 16419-16430,16434-16436, 16438-16440, 16442-16445, 16447-16455, 16457-16459,16461-16463, 16472-16474, 16477, 16479, 16481-16482, 16484-16489,16491-16493, 16495-16498, 16501-16503, 16505-16506, 16509, 16511-16513,16515-16517, 16520-16526, 16528-16529, 16531-16534, 16537-16541,16544-16545, 16547-16549, 16551-16556, 16558, 16560-16566,16568-16569,16571-16572, 16574, 16576-16585, 16588-16598, 16600-16602,16604-16608, 16611-16616, 16618, 16622-16627, 16629-16630, 16632-16636,16638-16642, 16645-16647, 16649-16655, 16657-16663, 16665-16671, 16673,16676-16679, 16681-16685, 16687-16692, 17204-17206, 17208-17209,17212-17213, 17215-17222, 17224-17230, 17232-17236, 17238-17239,17241-17252, 17256-17258, 17260-17262, 17264-17267, 17269-17277,17279-17281, 17283-17285, 17294-17296, 17299, 17301, 17304-17305,17307-17312, 17314-17316, 17318-17321, 17324-17326, 17328-17329, 17332,17334-17336, 17339-17341, 17344-17352, 17354-17355, 17357-17360,17363-17367, 17370-17371, 17373-17375, 17377-17382, 17384, 17386-17392,17394-17396, 17398-17399, 17401, 17403-17412, 17415-17425,17427-17429,17431-17435, 17438-17443, 17445, 17449-17454, 17456-17457, 17459-17463,17465-17469, 17472-17474, 17476-17482, 17484-17490, 17492-17498, 17500,17503-17506, 17508-17512, 17514- 15882-15887, 15889-15894, 15897-15900,15902, 15904-15908, 15910-15914, 15916-15928, 15930-15935, 15939-15947,15949-15951, 15953-15957, 15960-15966, 15968-15977, 15979-15983,15986-15992, 15997-15998, 16000-16003, 16005-16009, 16011, 16014-16020,16023-16031, 16035-16036, 16038, 16041, 16045-16048, 16054-16055,16059,16061-16063, 16065-16073, 16075-16078, 16080-16082, 16085-16088,16090-16091, 16093, 16095-16096, 16098-16100, 16102-16103, 16106,16108-16111, 16113-16116, 16118-16122, 16124-16127, 16129-16136,16138-16145,16147-16148, 16150-16154, 16157, 16159-16161, 16164-16170,16172-16177, 16181, 16184-16187, 16189-16198, 16200-16201, 16203,16206-16215, 16218-16230, 16694-16699, 16702-16705, 16707, 16709-16713,16715-16719, 16721-16733, 16735-16740, 16744-16752, 16754-16756,16758-16762, 16765-16766, 16768-16771, 16773-16782, 16784-16788,16791-16798, 16803-16804, 16806-16809, 16811-16815, 16817, 16820-16826,16829-16837, 16839, 16842-16843, 16845, 16848, 16852-16855, 16861-16863,16867, 16869-16871, 16873-16881, 16883-16886, 16888-16890, 16893-16897,16899-16900, 16902, 16904-16905, 16907-16908, 16910-16911, 16913-16916,16919, 16921-16924, 16926-16929, 16931-16939, 16941-16948, 16950-16957,16959-16960, 16962-16966, 16969, 16971-16973, 16976-16982, 16984-16989,16993-16994, 16997-17000, 17002-17011, 17013-17014, 17016, 17019, 17021-17519, 17521-17526, 17529-17532, 17534, 17536-17540, 17542-17546,17548-17560, 17562-17567, 17571-17579, 17581-17583, 17585-17589,17592-17593, 17595-17599, 17601-17610, 17612-17616, 17619-17626,17631-17633, 17635-17638, 17640-17644, 17646, 17649-17655, 17658-17666,17668, 17671-17672, 17674-17675, 17678, 17682-17685, 17691, 17693-17695,17699, 17701-17703, 17705-17714,17716-17719,17721-17723, 17726-17730,17732-17733, 17735, 17737-17738, 17740-17741, 17743-17745, 17747-17750,17754-17757, 17759-17762, 17764-17772, 17774-17781, 17783-17784,17786-17790, 17792-17793, 17795-17800, 17803, 17805-17807, 17810-17816,17818-17823, 17827-17828, 17831-17834,17836-17846, 17848- 16232, 16234,16236-16240, 16242-16247, 16249-16250, 16252, 16255, 17910-18038 17029,17032-17044, 17046, 17048, 17050-17055, 17057-17064, 17066-17068, 17070,17073,18039-18182 17850, 17852, 17855-17864, 17867-17879, 17881, 17883,17885-17890, 17892-17899, 17901-17903, 17905, 17907, 17909,18183-183227:93106106-7:93106605 (Intron 2) 18323-19086 19087-19860 19861-20640

The indicated locations listed in column 1 of the Table 1 are based ongnomAD v3.1 database and UCSC Genome Browser assembly ID: hg38,Sequencing/Assembly provider ID: Genome Reference Consortium HumanGRCh38.p12 (GCA_000001405.27). Assembly date: December 2013 initialrelease; December 2017 patch release 12.

The SNP details are indicated by the listed SNP ID Nos. (“rs numbers”),which are based on the NCBI 2018 database of Single NucleotidePolymorphisms (dbSNP)). The indicated DNA mutations are associated withTranscript Consequence NM_017654 as obtained from NCBI RefSeq genes.

Examples are provided below to facilitate a more complete understandingof the invention. The following examples illustrate the exemplary modesof making and practicing the invention. However, the scope of theinvention is not limited to specific embodiments disclosed in theseExamples, which are for purposes of illustration only.

EXPERIMENTAL DETAILS Example 1: SAMD9 Correction Anaylsis

Guide sequences comprising 17-50 contiguous nucleotides containingnucleotides in the sequence set forth in any one of SEQ ID NOs: 1-20640are screened for high on target activity using SpCas9 in HeLa cells. Ontarget activity is determined by DNA capillary electrophoresis analysis.

Example 2: Additional SAMD9 Editing Analysis

Germline gain of function mutations in sterile α motif domain-containingprotein 9 (SAMD9) enhance its physiologic growth-inhibitory function andcause MIRAGE syndrome, which is characterized by growth restrictionleading to bone marrow failure. To choose optimal RNA guide moleculesfor mutant allele elimination using a one-guide molecule strategy, whichtargets SNPs residing in the gene leading to protein truncation, or atwo-guide molecule strategy deleting the full gene or 3′UTR of SAMD9, 14different RNA guide molecules targeting nine (9) SNPs restricted toupstream of, downstream of, or within a coding region were screened forhigh on-target activity in HeLa and HSC cells (Table 2).

In HeLa cells, seven (7) different RNA guide moelcules targeting four(4) SNPs were screened by transfecting SpCas9 and a guide-expressing DNAmolecule. Briefly, screening was performed in a 96-well format with anSpCas9 coding plasmid (64 ng) co-transfected with a DNA plasmid thatexpresses a RNA guide molecule (20 ng) using JetOPTIMUS® reagent(Polyplus). Cells were harvested 72 hours post DNA transfection. Celllysis and genomic DNA extraction was performed in Quick extract(Lucigen) and endogenous genomic regions were amplified using specificprimers to measure on-target activity by next-generation sequencing(NGS) (FIG. 1 , Table 2).

Next, novel OMNI CRISPR nucleases with unique PAM requirements weretested for editing of upstream or coding region SNPs. These nucleaseswere tested in HeLa cells as described above. To this end, per each OMNICRISPR nuclease, the corresponding OMNI-P2A-mCherry expression vector(pmOMNI, Table 4) was transfected into HeLa cells together with sgRNAdesigned to target specific location in the human genome (guide sequenceportion, Table 2). At 72 hours cells were harvested, and half of thecells were used for quantification of transfection efficiency by FACSusing mCherry fluorescence as marker. The rest of the cells were lysed,and their genomic DNA content was used in a PCR reaction which amplifiedthe corresponding putative genomic targets. Amplicons were subjected toNGS and the resulting sequences were then used to calculate thepercentage of editing events in each target site. Short insertions ordeletions (indels) around the cut site are the typical outcome of repairof DNA ends following nuclease induced DNA cleavage. The calculation of% editing was therefore deduced from the fraction of indels containingsequences within each amplicon.

In addition, seven (7) additional, different RNA guide moleculestargeting five (5) SNPs relevant to both excision and a one-guidestrategy were screened in HSC cells. Briefly, 250 × 10³ HSC cells weremixed with preassembled RNPs composed of 105 pmole SpCas9 protein and120 pmole of a sgRNA comprising a 20-nucleotide guide sequence portion,specified in Table 2, mixed with 100 pmole of electroporation enhancer(IDT-1075916) and electroporated using P3 primary cell 4D-nucleofector XKit S (V4XP-3032, Lonza) by applying the DZ-100 program. A fraction ofcells were harvested 72 hours post electroporation and genomic DNA wasextracted to measure on-target activity by NGS. According to NGSanalysis, all RNA guide molecules (FIG. 2 , Table 2) depicted indelactivity ranging from 10% -90%. Editing of g5 and g7 were allelespecific (FIG. 3 ).

To test a one-guide molecule editing strategy of the mutant allele bytargeting a SNP residing in the coding region of the gene (e.g.rs10279499, rs78564070 or rs6965201), which will lead to indels orframeshifts in the coding sequence and truncated protein, U2OS cells,homozygous to rs 10279499, rs78564070 and rs6965201 SNPs, were editedwith an RNA guide molecule having one of four (4) different guidesequence portions. Briefly, 200 x 10³ U2OS cells were mixed withpreassembled RNPs composed of 105 pmole SpCas9 protein and 120 pmole ofa sgRNA comprising a 20-nucleotide guide sequence portion, specified inTable 2, mixed with 100 pmole of electroporation enhancer (IDT-1075916)and electroporated using SE primary cell 4D-nucleofector X Kit S(V4XC-1032, Lonza) by applying the DN-100 program. A fraction of cellswere harvested 72 hours post electroporation, genomic DNA was extracted,and an on-target editing activity of 45-96% was measured by NGS. Cellswere grown for an additional three (3) days and harvested for proteindegradation. SAMD9 protein levels were detected with anti-SAMD9 antibody(ab180575, Abcam) and anti-GAPDH (60004-1-lg, Protein-tech) was used fornormalization (FIGS. 3A, B). All guide sequence portions which depictedhigh editing efficiency resulted in significant decrease in SAMD9 levels(FIGS. 4A-4B) and can be used for a one-guide molecule strategy.

TABLE 2 20-nucleotide or 22-nucleotide long guide sequence portionsequences targeting SNPs located in SAMD9 region Genomic region SNPGuide Sequence Portion (gRNA) Name Guide Sequence Portion Sequence PAMregion Coding region rs10279499 g1 AUCUCUUGGGUCAUCCACAG (SEQ ID NO:9913) AGG g2 AUUUCUAUUACUGUCCUCUG (SEQ ID NO: 5746) UGG g30AUCUCUUGGGUCAUCCACAGAG (SEQ ID NO: 10003) GACAGTAA Coding regionrs78564070 g3 AGAGUAGAAAUCGUCUCAUU (SEQ ID NO: 10191) UGG g4AGAAAUCGUCUCAUUUGGUG (SEQ ID NO: 10189) UGG Coding region rs6965201 g5UAAUCUGGAAAUAAUCAUAU (SEQ ID NO: 10487) UGG Upstream rs6957832 g7GCAAGGCGGCAGCAAGCCUG (SEQ ID NO: 12525) GGG Upstream rs12668221 g9CAGAGUUGAGGUCUGUUUAA (SEQ ID NO: 11266) AGG g31 GCCAAGACCCUUUAAACAGACC(SEQ ID NO: 11391) TCAACTCT Downstream rs10953090 g23_altAGAAGCAGAAAGUUGAAUGG (SEQ ID NO: 9108) UGG g24_alt CAUAGAAGCAGAAAGUUGAA(SEQ ID NO: 9114) UGG Upstream rs12668221 g25 AGAGUUGAGGUCUGUUUAAA (SEQID NO: 11261) GGG g26 GAGGUCUGUUUAAAGGGUCU (SEQ ID NO: 11280) UGGUpstream rs12704664 g27 CCCUGUCUGACAGCUUUGAA (SEQ ID NO: 12657) AGGUpstream rs67885698 g28 UGGCGAGGCACGGCAAGGCA (SEQ ID NO: 12255) CGG g29GAGGCACGGCAAGGCACGGC (SEQ ID NO: 12233) GGG Upstream rs10229795 g32CUGAGUUUGUAUCUGCCACUAG (SEQ ID NO: 11808) AAAACAAT

TABLE 3 Novel nucleases sgRNA scaffold sequences, with each OMNI CRISPRnuclease also indicated with its PAM requirement OMNI CRISPR NucleasePAM Sequence sgRNA Scaffold Sequence OMNI-103 (SEQ ID NO:20646) with g31NNRACTGccaagacccUUUaaacagaccGUUUGAGAGUAGUGUAAgaaaUUACACUACAAGUUCAAAUAAAAAUUUAUUCAAAUCCAUUUGCUACAUUGUGUAGAAUUUAAAGAUCUGGCAACAGAUCUUUUUUU(SEQ ID NO: 20649) OMNI-120 (SEQ ID NO: 20647 with g32 NRRACCUgagUUUgUaUcUgccacUagGUUUGAGAGCCUUGUUAgaaaUAACAAGGCGAGUGCAAAUAAGGUUUAACCGAAUUCACCGUUUAUGGACCGCAUUGUGCGGAUUUUUU(SEQ ID NO: 20650) OMNI-138 (SEQ ID NO: 20648) with g30 NNNNGBNHAUCUCUUGGGUCAUCCACAGAGGUUGUAGUUCCCUAAUUAUgaaaACAAUUAGGUUACUAUGAUAAGGUAGUAUACCGCAAAGCUCUAACGCCUCAUCUUAAUGAUGGGGCGUUAUCUUUUUU(SEQ ID NO: 20651)

TABLE 4 OMNI CRISPR nuclease mammalian expression plasmid and elementsPlasmid Name Purpose Elements pmOMNI Expressing OMNI polypeptide in themammalian system CMV promoter - Kozak - SV40 NLS - OMNI ORF (humanoptimized) - HA - SV40 NLS - P2A - mCherry - bGH poly(A) signal

TABLE 4 Annex Element SEQ ID NO of Amino Acid Sequence SEQ ID NO of DNAsequence HA Tag SEQ ID NO: 20652 SEQ ID NO: 20656 NLS SEQ ID NO: 20653SEQ ID NO: 20657 P2A SEQ ID NO: 20654 SEQ ID NO: 20658 mCherry SEQ IDNO: 20655 SEQ ID NO: 20659

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1. A method for modifying in a cell a mutant allele of the sterile alphamotif domain containing 9 (SAMD9) gene having a mutation associated withMIRAGE syndrome, the method comprising introducing to the cell acomposition comprising: at least one CRISPR nuclease or a sequenceencoding a CRISPR nuclease; and a first RNA molecule comprising a guidesequence portion having 17-50 nucleotides or a nucleotide sequenceencoding the same, wherein a complex of the CRISPR nuclease and thefirst RNA molecule affects a double strand break in the mutant allele ofthe SAMD9 gene.
 2. The method of claim 1, wherein the first RNA moleculetargets the CRISPR nuclease to a SNP position of the mutant allele,wherein the SNP position is any one of rs10279499, rs201891812,rs73216083, rs542330750, rs7798225, rs10953089, rs10953090, rs10277338,rs71562815, rs12333976, rs3839837, rs78564070, rs6965201, rs6969691,rs2374627, rs12668221, rs28673511, rs10229795, rs7785869, rs67885698,rs6957832 and rs12704664; wherein the guide sequence portion of thefirst RNA molecule comprises 17-50 contiguous nucleotides containingnucleotides in the sequence set forth in any one of SEQ ID NO: 9913, SEQID NOs: 1-9912, or SEQ ID NOs: 9914-20640 that targets a SNP position ofthe mutant allele; wherein the SNP position is in an exon of the SAMD9mutant allele; and/or wherein the SNP position contains a heterozygousSNP. 3-6. (canceled)
 7. The method of claim 1, wherein the first RNAmolecule targets the CRISPR nuclease to the mutation associated withMIRAGE syndrome, wherein the mutation associated with MIRAGE syndrome isany one of 7:93101391 C G, 7:93101435 GA, 7:93101512 C T, 7:93101540 CA, 7:93101615 T C, 7:93101761 AGTT A, 7:93101900 G A, 7:93102220 C T,7:93102221 G A, 7:93102242 G T, 7:93102259 G A, 7:93102368 T C,7:93102514 G A, 7:93102593 G A, 7:93102692 C G, 7:93102717 G T,7:93103150 AT GA, 7:93103151 T C, 7:93103153 C T, 7:93103178 C T,7:93103253 C A, 7:93103393 C T, 7:93103588 C CT, 7:93103598 T A,7:93103628 G A, 7:93103679 C T, 7:93103765 G A, 7:93103772 G T,7:93103793 C T, 7:93103851 G T, 7:93103900 A G, 7:93103916 T C,7:93103933 G T, 7:93103938 GT G, 7:93104044 C T, 7:93104176 A G,7:93104296 ATT A, 7:93104449 T A, 7:93104694 TAC GCA, 7:93104695 AC GA,7:93104722 C T, 7:93105043 A G, 7:93105103 A G, 7:93105122 G A,7:93105295 A G, 7:93105436 C T, 7:93105485 T G, 7:93105638 G A,7:93105781 C T, 7:93105965 CT C, 7:93106002 GT G, 7:93106003 T A, and7:93106096 A G; and/or wherein the guide sequence portion of the firstRNA molecule comprises 17-50 contiguous nucleotides containingnucleotides in the sequence set forth in any one of SEQ ID NOs: 1-20640that targets a mutation associated with MIRAGE syndrome. 8-9. (canceled)10. The method of claim 7, further comprising introduction of a donormolecule that encodes a synthetic splice site.
 11. The method of claim1, further comprising introducing to the cell a second RNA moleculecomprising a guide sequence portion having 17-50 nucleotides or anucleotide sequence encoding the same, wherein a complex of the secondRNA molecule and a CRISPR nuclease affects a second double strand breakin the SAMD9 gene.
 12. The method of claim 11, wherein the guidesequence portion of the second RNA molecule comprises 17-50 contiguousnucleotides containing nucleotides in the sequence set forth in any oneof SEQ ID NOs: 1-20640 other than the sequence of the first RNAmolecule.
 13. The method of claim 11, wherein the second RNA moleculecomprises a non-discriminatory guide portion that targets bothfunctional and mutated SAMD9 alleles.
 14. The method of claim 11,wherein the second RNA molecule comprises a non-discriminatory guideportion that targets any one of a SAMD9 untranslated region (UTR), anintergenic region upstream of SAMD9, an intergenic region downstream ofSAMD9, or Intron 2 of SAMD9; wherein the second RNA molecule comprises anon-discriminatory guide portion that targets a sequence that is locatedwithin a genomic range selected from any one of 7:93100828 to7:93101327, 7:93099521 to 7:93100020, 7:93099413 to 7:93099913, or7:93106106 to 7:93106605; and/or wherein the second RNA moleculecomprises a non-discriminatory guide portion that targets a sequencethat is located up to 500 base pairs from the sequence targeted by thefirst RNA molecule. 15-16. (canceled)
 17. The method of claim 11,wherein a portion of an exon is excised from the mutant allele of theSAMD9 gene.
 18. The method of claim 11, wherein the first RNA moleculetargets a SNP position in the 3′ UTR of the mutated allele, and thesecond RNA molecule comprises a non-discriminatory guide portion thattargets downstream of a polyadenylation signal sequence that is commonto both a functional allele and the mutant allele of the SAMD9 gene; orwherein the first RNA molecule targets a SNP position downstream of apolyadenylation signal of the mutated allele, and the second RNAmolecule comprises a non-discriminatory guide portion that targets asequence upstream of a polyadenylation signal that is common to both afunctional allele and the mutant allele of the SAMD9 gene. 19.(canceled)
 20. The method of claim 18, wherein the polyadenylationsignal is excised from the mutant allele of the SAMD9 gene.
 21. Amodified cell obtained by the method of claim
 1. 22. A first RNAmolecule comprising a guide sequence portion having 17-50 contiguousnucleotides containing nucleotides in the sequence set forth in any oneof SEQ ID NOs: 1-20640.
 23. A composition comprising the first RNAmolecule of claim 22 and at least one CRISPR nuclease.
 24. Thecomposition of claim 23, further comprising a second RNA moleculecomprising a guide sequence portion having 17-50 contiguous nucleotides,wherein the second RNA molecule targets a SAMD9 allele, and wherein theguide sequence portion of the second RNA molecule is a differentsequence from the sequence of the guide sequence portion of the firstRNA molecule.
 25. The composition of claim 24, wherein the guidesequence portion of the second RNA molecule comprises 17-50 contiguousnucleotides containing nucleotides in the sequence set forth in any oneof SEQ ID NOs: 1-20640 other than the sequence of the first RNAmolecule.
 26. A method for inactivating a mutant SAMD9 allele in a cell,the method comprising delivering to the cell the composition of claim22.
 27. A method for treating MIRAGE syndrome, the method comprisingdelivering to a cell of a subject having MIRAGE syndrome the compositionof claim
 22. 28. (canceled)
 29. A medicament comprising the compositionof claim 23 for use in inactivating a mutant SAMD9 allele in a cell,wherein the medicament is administered by delivering to the cell thecomposition of claim
 23. 30. (canceled)
 31. A medicament comprising thecomposition of claim 23 for use in treating ameliorating or preventingMIRAGE syndrome, wherein the medicament is administered by delivering toa cell of a subject having or at risk of having MIRAGE syndrome thecomposition of claim 23.